From 4566b3d46e0e80042552f1e5373a2416a6ffaf5e Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Thu, 30 Nov 2023 08:23:22 -0500
Subject: [PATCH 01/37] Move nf-test files and container definitions

---
 conf/container.config                               |  3 ---
 modules/local/plot_run_gantt/main.nf                |  1 +
 modules/local/plot_run_gantt/tests/nextflow.config  |  2 --
 modules/local/seqera_runs_dump/main.nf              |  1 +
 .../local/seqera_runs_dump/tests/nextflow.config    |  1 -
 nextflow.config                                     | 13 +++++--------
 tests/nextflow.config                               |  5 -----
 .../nf_aggregate/tests}/main.nf.test                |  2 +-
 {tests => workflows/nf_aggregate/tests}/tags.yml    |  0
 9 files changed, 8 insertions(+), 20 deletions(-)
 delete mode 100644 conf/container.config
 delete mode 100644 modules/local/plot_run_gantt/tests/nextflow.config
 delete mode 100644 modules/local/seqera_runs_dump/tests/nextflow.config
 delete mode 100644 tests/nextflow.config
 rename {tests => workflows/nf_aggregate/tests}/main.nf.test (88%)
 rename {tests => workflows/nf_aggregate/tests}/tags.yml (100%)

diff --git a/conf/container.config b/conf/container.config
deleted file mode 100644
index aa02ee2..0000000
--- a/conf/container.config
+++ /dev/null
@@ -1,3 +0,0 @@
-process { withName: 'NF_AGGREGATE:SEQERA_RUNS_DUMP' { container = 'quay.io/seqeralabs/nf-aggregate:tower-cli-0.9.0--2cb0f2e9d85d026b' } }
-process { withName: 'NF_AGGREGATE:MULTIQC' { container = 'quay.io/seqeralabs/nf-aggregate:multiqc--545f544898344f7d' } }
-process { withName: 'NF_AGGREGATE:PLOT_RUN_GANTT' { container = 'quay.io/seqeralabs/nf-aggregate:click-8.0.1_pandas-1.1.5_plotly_express-0.4.1_typing-3.10.0.0--342dabfe6548a051' } }
diff --git a/modules/local/plot_run_gantt/main.nf b/modules/local/plot_run_gantt/main.nf
index 9f9a0fe..7413640 100644
--- a/modules/local/plot_run_gantt/main.nf
+++ b/modules/local/plot_run_gantt/main.nf
@@ -1,6 +1,7 @@
 process PLOT_RUN_GANTT {
     tag "$meta.id"
     conda 'click=8.0.1 pandas=1.1.5 plotly_express=0.4.1 typing=3.10.0.0'
+    container 'seqeralabs/nf-aggregate:click-8.0.1_pandas-1.1.5_plotly_express-0.4.1_typing-3.10.0.0--342dabfe6548a051'
 
     input:
     tuple val(meta), path(run_dump)
diff --git a/modules/local/plot_run_gantt/tests/nextflow.config b/modules/local/plot_run_gantt/tests/nextflow.config
deleted file mode 100644
index a7b7f88..0000000
--- a/modules/local/plot_run_gantt/tests/nextflow.config
+++ /dev/null
@@ -1,2 +0,0 @@
-process { withName: 'SEQERA_RUNS_DUMP' { container = 'public.ecr.aws/seqera-labs/wave/containers:tower-cli-0.9.0--2cb0f2e9d85d026b' } }
-process { withName: 'PLOT_RUN_GANTT' { container = 'quay.io/seqeralabs/nf-aggregate:click-8.0.1_pandas-1.1.5_plotly_express-0.4.1_typing-3.10.0.0--342dabfe6548a051' } }
diff --git a/modules/local/seqera_runs_dump/main.nf b/modules/local/seqera_runs_dump/main.nf
index 4ea74c9..1628beb 100644
--- a/modules/local/seqera_runs_dump/main.nf
+++ b/modules/local/seqera_runs_dump/main.nf
@@ -3,6 +3,7 @@ include { getRunMetadata } from './functions'
 process SEQERA_RUNS_DUMP {
     tag "$meta.id"
     conda 'tower-cli=0.9.0'
+    container 'seqeralabs/nf-aggregate:tower-cli-0.9.0--2cb0f2e9d85d026b'
 
     input:
     val meta
diff --git a/modules/local/seqera_runs_dump/tests/nextflow.config b/modules/local/seqera_runs_dump/tests/nextflow.config
deleted file mode 100644
index e1348a5..0000000
--- a/modules/local/seqera_runs_dump/tests/nextflow.config
+++ /dev/null
@@ -1 +0,0 @@
-process { withName: 'SEQERA_RUNS_DUMP' { container = 'quay.io/seqeralabs/nf-aggregate:tower-cli-0.9.0--2cb0f2e9d85d026b' } }
diff --git a/nextflow.config b/nextflow.config
index a42e39d..aafbd8d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -58,7 +58,7 @@ profiles {
     wave {
         wave.enabled = true
         wave.strategy = ['conda']
-        wave.build.repository = 'public.ecr.aws/seqera-labs/wave/containers'
+        wave.build.repository = 'quay.io/seqeralabs/nf-aggregate'
         wave.freeze = true   
     }
     test_full {
@@ -157,10 +157,10 @@ profiles {
 // Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
 // Set to your registry if you have a mirror of containers
-apptainer.registry   = 'public.ecr.aws/seqera-labs/wave/containers'
-docker.registry      = 'public.ecr.aws/seqera-labs/wave/containers'
-podman.registry      = 'public.ecr.aws/seqera-labs/wave/containers'
-singularity.registry = 'public.ecr.aws/seqera-labs/wave/containers'
+apptainer.registry   = 'quay.io'
+docker.registry      = 'quay.io'
+podman.registry      = 'quay.io'
+singularity.registry = 'quay.io'
 
 // Nextflow plugins
 plugins {
@@ -182,9 +182,6 @@ env {
 // Load Nextflow config for nf_aggregate workflow
 includeConfig 'workflows/nf_aggregate/nextflow.config'
 
-// Load container config for nf_aggregate workflow
-includeConfig 'conf/container.config'
-
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
diff --git a/tests/nextflow.config b/tests/nextflow.config
deleted file mode 100644
index c19b1ad..0000000
--- a/tests/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for running tests
-========================================================================================
-*/
diff --git a/tests/main.nf.test b/workflows/nf_aggregate/tests/main.nf.test
similarity index 88%
rename from tests/main.nf.test
rename to workflows/nf_aggregate/tests/main.nf.test
index 403d653..6f828f2 100644
--- a/tests/main.nf.test
+++ b/workflows/nf_aggregate/tests/main.nf.test
@@ -10,7 +10,7 @@ nextflow_pipeline {
 
         when {
             params {
-                outdir     = "results"
+                outdir = "results"
             }
         }
 
diff --git a/tests/tags.yml b/workflows/nf_aggregate/tests/tags.yml
similarity index 100%
rename from tests/tags.yml
rename to workflows/nf_aggregate/tests/tags.yml

From d27f656372c5f2ed684f921c468e1b6cbd1cc1d2 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 30 Nov 2023 14:03:47 +0000
Subject: [PATCH 02/37] Fix CI test triggers (which weren't active on PR)

---
 .github/workflows/ci.yml                          | 11 +++++++----
 modules/local/plot_run_gantt/tests/main.nf.test   |  1 -
 modules/local/seqera_runs_dump/tests/main.nf.test |  1 -
 nf-test.config                                    |  2 +-
 4 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1122e3f..d00e809 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,12 +1,15 @@
 name: nf-aggregate CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
-    types: [published]
+    types:
+      - published
+  merge_group:
+    types:
+      - checks_requested
+    branches:
+      - master
 
 env:
   NXF_ANSI_LOG: false
diff --git a/modules/local/plot_run_gantt/tests/main.nf.test b/modules/local/plot_run_gantt/tests/main.nf.test
index 372198b..3d56dbf 100644
--- a/modules/local/plot_run_gantt/tests/main.nf.test
+++ b/modules/local/plot_run_gantt/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process PLOT_RUN_GANTT"
     script "../main.nf"
     process "PLOT_RUN_GANTT"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_local"
diff --git a/modules/local/seqera_runs_dump/tests/main.nf.test b/modules/local/seqera_runs_dump/tests/main.nf.test
index 71fe5f2..9d90498 100644
--- a/modules/local/seqera_runs_dump/tests/main.nf.test
+++ b/modules/local/seqera_runs_dump/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process SEQERA_RUNS_DUMP"
     script "../main.nf"
     process "SEQERA_RUNS_DUMP"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_local"
diff --git a/nf-test.config b/nf-test.config
index cb656b9..0799cb4 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir "/tmp"
+    workDir ".nf-test"
 
     // location of library folder that is added automatically to the classpath
     libDir "lib/"

From 0d8c84ce9545f7b87a28865f3286ebb5afa4ab28 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 30 Nov 2023 14:04:29 +0000
Subject: [PATCH 03/37] Fix mistake in CI

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d00e809..42aa3a7 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -19,7 +19,6 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  test:
   changes:
     name: Check for changes
     runs-on: ubuntu-latest
@@ -37,6 +36,7 @@ jobs:
         id: filter
         with:
           filters: ".github/tags.yml"
+
   nf-test:
     name: nf-test ${{ matrix.tags }} ${{ matrix.profile }}
     needs: [changes]

From a0af0a4d9127a71b903857b20ea0b5b9f457ee02 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 30 Nov 2023 14:59:31 +0000
Subject: [PATCH 04/37] Add FASTQC for testing purposes

---
 .gitignore                                    |  2 +-
 modules.json                                  |  5 ++
 modules/nf-core/fastqc/environment.yml        |  7 +++
 modules/nf-core/fastqc/main.nf                | 55 ++++++++++++++++++
 modules/nf-core/fastqc/meta.yml               | 57 +++++++++++++++++++
 modules/nf-core/fastqc/tests/main.nf.test     | 41 +++++++++++++
 .../nf-core/fastqc/tests/main.nf.test.snap    | 10 ++++
 modules/nf-core/fastqc/tests/tags.yml         |  2 +
 8 files changed, 178 insertions(+), 1 deletion(-)
 create mode 100644 modules/nf-core/fastqc/environment.yml
 create mode 100644 modules/nf-core/fastqc/main.nf
 create mode 100644 modules/nf-core/fastqc/meta.yml
 create mode 100644 modules/nf-core/fastqc/tests/main.nf.test
 create mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/fastqc/tests/tags.yml

diff --git a/.gitignore b/.gitignore
index 089a407..2eef655 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,4 +6,4 @@ results/
 testing/
 testing*
 *.pyc
-.nf-test
+.nf-test*
diff --git a/modules.json b/modules.json
index 01231a9..963932d 100644
--- a/modules.json
+++ b/modules.json
@@ -5,6 +5,11 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "1537442a7be4a78efa3d1ff700a923c627bbda5d",
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
new file mode 100644
index 0000000..1787b38
--- /dev/null
+++ b/modules/nf-core/fastqc/environment.yml
@@ -0,0 +1,7 @@
+name: fastqc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
new file mode 100644
index 0000000..50e59f2
--- /dev/null
+++ b/modules/nf-core/fastqc/main.nf
@@ -0,0 +1,55 @@
+process FASTQC {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
+        'biocontainers/fastqc:0.12.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.zip") , emit: zip
+    path  "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Make list of old name and new name pairs to use for renaming in the bash while loop
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    """
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+
+    fastqc \\
+        $args \\
+        --threads $task.cpus \\
+        $renamed_files
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+    touch ${prefix}.zip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
new file mode 100644
index 0000000..ee5507e
--- /dev/null
+++ b/modules/nf-core/fastqc/meta.yml
@@ -0,0 +1,57 @@
+name: fastqc
+description: Run FastQC on sequenced reads
+keywords:
+  - quality control
+  - qc
+  - adapters
+  - fastq
+tools:
+  - fastqc:
+      description: |
+        FastQC gives general quality metrics about your reads.
+        It provides information about the quality score distribution
+        across your reads, the per base sequence content (%A/C/G/T).
+        You get information about adapter contamination and other
+        overrepresented sequences.
+      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+      licence: ["GPL-2.0-only"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - html:
+      type: file
+      description: FastQC report
+      pattern: "*_{fastqc.html}"
+  - zip:
+      type: file
+      description: FastQC report archive
+      pattern: "*_{fastqc.zip}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@grst"
+  - "@ewels"
+  - "@FelixKrueger"
+maintainers:
+  - "@drpatelh"
+  - "@grst"
+  - "@ewels"
+  - "@FelixKrueger"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
new file mode 100644
index 0000000..6437a14
--- /dev/null
+++ b/modules/nf-core/fastqc/tests/main.nf.test
@@ -0,0 +1,41 @@
+nextflow_process {
+
+    name "Test Process FASTQC"
+    script "../main.nf"
+    process "FASTQC"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fastqc"
+
+    test("Single-Read") {
+
+        when {
+            params {
+                outdir   = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
+            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
+            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
+            { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" },
+            { assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
+            { assert snapshot(process.out.versions).match("versions") },
+            { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
new file mode 100644
index 0000000..636a32c
--- /dev/null
+++ b/modules/nf-core/fastqc/tests/main.nf.test.snap
@@ -0,0 +1,10 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
+            ]
+        ],
+        "timestamp": "2023-10-09T23:40:54+0000"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
new file mode 100644
index 0000000..7834294
--- /dev/null
+++ b/modules/nf-core/fastqc/tests/tags.yml
@@ -0,0 +1,2 @@
+fastqc:
+  - modules/nf-core/fastqc/**

From e50384e7e6e11b1916529fd4885358d01d7f0bcc Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 30 Nov 2023 16:49:08 +0000
Subject: [PATCH 05/37] Load test data

---
 nf-test.config        | 4 ++--
 tests/nextflow.config | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)
 create mode 100644 tests/nextflow.config

diff --git a/nf-test.config b/nf-test.config
index 0799cb4..48e26bd 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,13 +3,13 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir ".nf-test"
+    workDir "/tmp"
 
     // location of library folder that is added automatically to the classpath
     libDir "lib/"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "nextflow.config"
+    configFile "tests/nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 0000000..fec66b4
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1 @@
+includeConfig 'https://raw.githubusercontent.com/nf-core/modules/47ad5f5402a5125c6c6f6107abc9a8732ce7dd12/tests/config/test_data.config'
\ No newline at end of file

From fad7a36969acc6729bf59863d155e926e0ffb566 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 30 Nov 2023 17:33:24 +0000
Subject: [PATCH 06/37] Trying to load an extra param into tests

---
 modules/local/plot_run_gantt/tests/main.nf.test   | 3 +++
 modules/local/seqera_runs_dump/tests/main.nf.test | 3 +++
 nf-test.config                                    | 2 +-
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/modules/local/plot_run_gantt/tests/main.nf.test b/modules/local/plot_run_gantt/tests/main.nf.test
index 3d56dbf..5c8b6f6 100644
--- a/modules/local/plot_run_gantt/tests/main.nf.test
+++ b/modules/local/plot_run_gantt/tests/main.nf.test
@@ -23,6 +23,9 @@ nextflow_process {
         }
 
         when {
+            params {
+                publish_dir_mode   = "copy"
+            }
             process {
 
                 """
diff --git a/modules/local/seqera_runs_dump/tests/main.nf.test b/modules/local/seqera_runs_dump/tests/main.nf.test
index 9d90498..1247025 100644
--- a/modules/local/seqera_runs_dump/tests/main.nf.test
+++ b/modules/local/seqera_runs_dump/tests/main.nf.test
@@ -11,6 +11,9 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
+            params {
+                publish_dir_mode   = "copy"
+            }
             process {
                 """
                 input[0] = ['id': '4Bi5xBK6E2Nbhj', 'workspace': 'community/showcase']
diff --git a/nf-test.config b/nf-test.config
index 48e26bd..fc55554 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir "/tmp"
+    workDir ".nf-test"
 
     // location of library folder that is added automatically to the classpath
     libDir "lib/"

From 4fdb0501166e6c48665597b4be88408cc8b1ae92 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 1 Dec 2023 16:50:45 +0000
Subject: [PATCH 07/37] Move pipeline level test back to pipeline folder

---
 {workflows/nf_aggregate/tests => tests}/main.nf.test | 2 +-
 {workflows/nf_aggregate/tests => tests}/tags.yml     | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename {workflows/nf_aggregate/tests => tests}/main.nf.test (90%)
 rename {workflows/nf_aggregate/tests => tests}/tags.yml (100%)

diff --git a/workflows/nf_aggregate/tests/main.nf.test b/tests/main.nf.test
similarity index 90%
rename from workflows/nf_aggregate/tests/main.nf.test
rename to tests/main.nf.test
index 6f828f2..a87e57d 100644
--- a/workflows/nf_aggregate/tests/main.nf.test
+++ b/tests/main.nf.test
@@ -1,6 +1,6 @@
 nextflow_pipeline {
 
-    name "Test Workflow main.nf"
+    name "Test Pipeline main.nf"
     script "../main.nf"
 
     tag "pipeline"
diff --git a/workflows/nf_aggregate/tests/tags.yml b/tests/tags.yml
similarity index 100%
rename from workflows/nf_aggregate/tests/tags.yml
rename to tests/tags.yml

From 6b0f457375ddd49682f59f9494e9f71be89c68d6 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Fri, 1 Dec 2023 16:53:07 +0000
Subject: [PATCH 08/37] Remove publish_dir_mode use because it broke stuff

---
 modules/local/plot_run_gantt/nextflow.config   | 1 -
 modules/local/seqera_runs_dump/nextflow.config | 1 -
 2 files changed, 2 deletions(-)

diff --git a/modules/local/plot_run_gantt/nextflow.config b/modules/local/plot_run_gantt/nextflow.config
index 2b2ebb6..f2f794c 100644
--- a/modules/local/plot_run_gantt/nextflow.config
+++ b/modules/local/plot_run_gantt/nextflow.config
@@ -2,7 +2,6 @@ process {
     withName: 'PLOT_RUN_GANTT' {
         publishDir = [
             path: { "${params.outdir}/${meta.projectName?.replace("/", "_") ?: ""}/gantt" },
-            mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
diff --git a/modules/local/seqera_runs_dump/nextflow.config b/modules/local/seqera_runs_dump/nextflow.config
index 963db9a..8e79a50 100644
--- a/modules/local/seqera_runs_dump/nextflow.config
+++ b/modules/local/seqera_runs_dump/nextflow.config
@@ -4,7 +4,6 @@ process {
         ext.args2 = { params.skip_run_gantt ? '' : '--add-task-logs --add-fusion-logs' }
         publishDir = [
             path: { "${params.outdir}/${metaOut?.projectName?.replace("/", "_") ?: ""}/runs_dump" },
-            mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.json') ? null : filename }
         ]
     }

From cb63b7ac62780aeab441db927e03001bf22b6831 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Dec 2023 13:24:10 -0500
Subject: [PATCH 09/37] Remove FastQC module

---
 modules.json                                  |  5 --
 modules/nf-core/fastqc/environment.yml        |  7 ---
 modules/nf-core/fastqc/main.nf                | 55 ------------------
 modules/nf-core/fastqc/meta.yml               | 57 -------------------
 modules/nf-core/fastqc/tests/main.nf.test     | 41 -------------
 .../nf-core/fastqc/tests/main.nf.test.snap    | 10 ----
 modules/nf-core/fastqc/tests/tags.yml         |  2 -
 7 files changed, 177 deletions(-)
 delete mode 100644 modules/nf-core/fastqc/environment.yml
 delete mode 100644 modules/nf-core/fastqc/main.nf
 delete mode 100644 modules/nf-core/fastqc/meta.yml
 delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test
 delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/fastqc/tests/tags.yml

diff --git a/modules.json b/modules.json
index 963932d..01231a9 100644
--- a/modules.json
+++ b/modules.json
@@ -5,11 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"]
-                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "1537442a7be4a78efa3d1ff700a923c627bbda5d",
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
deleted file mode 100644
index 1787b38..0000000
--- a/modules/nf-core/fastqc/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: fastqc
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
deleted file mode 100644
index 50e59f2..0000000
--- a/modules/nf-core/fastqc/main.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-process FASTQC {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' :
-        'biocontainers/fastqc:0.12.1--hdfd78af_0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    // Make list of old name and new name pairs to use for renaming in the bash while loop
-    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
-    """
-    printf "%s %s\\n" $rename_to | while read old_name new_name; do
-        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
-    done
-
-    fastqc \\
-        $args \\
-        --threads $task.cpus \\
-        $renamed_files
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.html
-    touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
deleted file mode 100644
index ee5507e..0000000
--- a/modules/nf-core/fastqc/meta.yml
+++ /dev/null
@@ -1,57 +0,0 @@
-name: fastqc
-description: Run FastQC on sequenced reads
-keywords:
-  - quality control
-  - qc
-  - adapters
-  - fastq
-tools:
-  - fastqc:
-      description: |
-        FastQC gives general quality metrics about your reads.
-        It provides information about the quality score distribution
-        across your reads, the per base sequence content (%A/C/G/T).
-        You get information about adapter contamination and other
-        overrepresented sequences.
-      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-      licence: ["GPL-2.0-only"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
-  - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@grst"
-  - "@ewels"
-  - "@FelixKrueger"
-maintainers:
-  - "@drpatelh"
-  - "@grst"
-  - "@ewels"
-  - "@FelixKrueger"
diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
deleted file mode 100644
index 6437a14..0000000
--- a/modules/nf-core/fastqc/tests/main.nf.test
+++ /dev/null
@@ -1,41 +0,0 @@
-nextflow_process {
-
-    name "Test Process FASTQC"
-    script "../main.nf"
-    process "FASTQC"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "fastqc"
-
-    test("Single-Read") {
-
-        when {
-            params {
-                outdir   = "$outputDir"
-            }
-            process {
-                """
-                input[0] = [
-                    [ id: 'test', single_end:true ],
-                    [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-                    ]
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll (
-            { assert process.success },
-            // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
-            // looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
-            // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
-            { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" },
-            { assert path(process.out.html.get(0).get(1)).getText().contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
-            { assert snapshot(process.out.versions).match("versions") },
-            { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" }
-            )
-        }
-    }
-}
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
deleted file mode 100644
index 636a32c..0000000
--- a/modules/nf-core/fastqc/tests/main.nf.test.snap
+++ /dev/null
@@ -1,10 +0,0 @@
-{
-    "versions": {
-        "content": [
-            [
-                "versions.yml:md5,e1cc25ca8af856014824abd842e93978"
-            ]
-        ],
-        "timestamp": "2023-10-09T23:40:54+0000"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
deleted file mode 100644
index 7834294..0000000
--- a/modules/nf-core/fastqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-fastqc:
-  - modules/nf-core/fastqc/**

From 8d271f89955dec44ac3031553f96f794ba8e28c3 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Dec 2023 13:25:03 -0500
Subject: [PATCH 10/37] Add wave.strategy precedence

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index aafbd8d..b148b09 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -57,7 +57,7 @@ profiles {
     }
     wave {
         wave.enabled = true
-        wave.strategy = ['conda']
+        wave.strategy = ['conda', 'container', 'dockerfile', 'spack']
         wave.build.repository = 'quay.io/seqeralabs/nf-aggregate'
         wave.freeze = true   
     }

From cf8b31ebf77a0f823f1e7d9a4de0c8aaa9b7a724 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Dec 2023 13:32:45 -0500
Subject: [PATCH 11/37] Remove Conda profile from testing in CI

---
 .github/workflows/ci.yml | 17 -----------------
 1 file changed, 17 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 42aa3a7..535b431 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -53,7 +53,6 @@ jobs:
         tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
         profile:
           - "docker"
-          - "conda"
 
     steps:
       - name: Check out pipeline code
@@ -64,22 +63,6 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Set up miniconda
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          channels: conda-forge,bioconda,defaults
-          python-version: ${{ matrix.python-version }}
-
-      - name: Conda setup
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
       - name: Cache nf-test installation
         id: cache-software
         uses: actions/cache@v3

From e7216d016c551499234710f0d9631c3c65f2a2ff Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Dec 2023 13:36:42 -0500
Subject: [PATCH 12/37] Add publish_dir_mode parameter back

---
 modules/local/plot_run_gantt/nextflow.config      | 1 +
 modules/local/plot_run_gantt/tests/main.nf.test   | 2 +-
 modules/local/seqera_runs_dump/nextflow.config    | 1 +
 modules/local/seqera_runs_dump/tests/main.nf.test | 2 +-
 4 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/local/plot_run_gantt/nextflow.config b/modules/local/plot_run_gantt/nextflow.config
index f2f794c..2b2ebb6 100644
--- a/modules/local/plot_run_gantt/nextflow.config
+++ b/modules/local/plot_run_gantt/nextflow.config
@@ -2,6 +2,7 @@ process {
     withName: 'PLOT_RUN_GANTT' {
         publishDir = [
             path: { "${params.outdir}/${meta.projectName?.replace("/", "_") ?: ""}/gantt" },
+            mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
diff --git a/modules/local/plot_run_gantt/tests/main.nf.test b/modules/local/plot_run_gantt/tests/main.nf.test
index 5c8b6f6..bacc703 100644
--- a/modules/local/plot_run_gantt/tests/main.nf.test
+++ b/modules/local/plot_run_gantt/tests/main.nf.test
@@ -24,7 +24,7 @@ nextflow_process {
 
         when {
             params {
-                publish_dir_mode   = "copy"
+                publish_dir_mode = "copy"
             }
             process {
 
diff --git a/modules/local/seqera_runs_dump/nextflow.config b/modules/local/seqera_runs_dump/nextflow.config
index 8e79a50..963db9a 100644
--- a/modules/local/seqera_runs_dump/nextflow.config
+++ b/modules/local/seqera_runs_dump/nextflow.config
@@ -4,6 +4,7 @@ process {
         ext.args2 = { params.skip_run_gantt ? '' : '--add-task-logs --add-fusion-logs' }
         publishDir = [
             path: { "${params.outdir}/${metaOut?.projectName?.replace("/", "_") ?: ""}/runs_dump" },
+            mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.json') ? null : filename }
         ]
     }
diff --git a/modules/local/seqera_runs_dump/tests/main.nf.test b/modules/local/seqera_runs_dump/tests/main.nf.test
index 1247025..ccce4ce 100644
--- a/modules/local/seqera_runs_dump/tests/main.nf.test
+++ b/modules/local/seqera_runs_dump/tests/main.nf.test
@@ -12,7 +12,7 @@ nextflow_process {
 
         when {
             params {
-                publish_dir_mode   = "copy"
+                publish_dir_mode = "copy"
             }
             process {
                 """

From 36b9cd8920a4e3fc7e1aa6977bc7555d83876f17 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Dec 2023 18:05:27 -0500
Subject: [PATCH 13/37] Remove lib path

---
 nf-test.config | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/nf-test.config b/nf-test.config
index fc55554..c0ca9e3 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -5,9 +5,6 @@ config {
     // nf-test directory including temporary files for each test
     workDir ".nf-test"
 
-    // location of library folder that is added automatically to the classpath
-    libDir "lib/"
-
     // location of an optional nextflow.config file specific for executing tests
     configFile "tests/nextflow.config"
 

From 24751945f63fcf8375b0ad11d65730a6de21f276 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Fri, 1 Dec 2023 18:08:16 -0500
Subject: [PATCH 14/37] Remove config for test data

---
 nf-test.config        | 2 +-
 tests/nextflow.config | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)
 delete mode 100644 tests/nextflow.config

diff --git a/nf-test.config b/nf-test.config
index c0ca9e3..2f5050c 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -6,7 +6,7 @@ config {
     workDir ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "tests/nextflow.config"
+    configFile "nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
diff --git a/tests/nextflow.config b/tests/nextflow.config
deleted file mode 100644
index fec66b4..0000000
--- a/tests/nextflow.config
+++ /dev/null
@@ -1 +0,0 @@
-includeConfig 'https://raw.githubusercontent.com/nf-core/modules/47ad5f5402a5125c6c6f6107abc9a8732ce7dd12/tests/config/test_data.config'
\ No newline at end of file

From 031c97aafa6143b051e88c567e5cae957d77a16c Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Mon, 4 Dec 2023 15:25:29 +0000
Subject: [PATCH 15/37] Add workflow tests

---
 workflows/nf_aggregate/tests/main.nf.test     | 38 +++++++++++++++++++
 .../nf_aggregate/tests/main.nf.test.snap      | 33 ++++++++++++++++
 workflows/nf_aggregate/tests/tags.yml         |  2 +
 3 files changed, 73 insertions(+)
 create mode 100644 workflows/nf_aggregate/tests/main.nf.test
 create mode 100644 workflows/nf_aggregate/tests/main.nf.test.snap
 create mode 100644 workflows/nf_aggregate/tests/tags.yml

diff --git a/workflows/nf_aggregate/tests/main.nf.test b/workflows/nf_aggregate/tests/main.nf.test
new file mode 100644
index 0000000..9585439
--- /dev/null
+++ b/workflows/nf_aggregate/tests/main.nf.test
@@ -0,0 +1,38 @@
+nextflow_workflow {
+
+    name "Test Workflow NF_AGGREGATE"
+    script "../main.nf"
+    workflow "NF_AGGREGATE"
+
+    tag "workflows"
+    tag "workflows_nf_aggregate"
+
+    stage {
+        symlink "workflows/nf_aggregate/assets/multiqc_config.yml"
+    }
+
+    test("Should run without failures") {
+
+        when {
+            workflow {
+                """
+                input[0] = ['id': '4Bi5xBK6E2Nbhj', 'workspace': 'community/showcase']
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert snapshot(
+                    workflow.out.multiqc_report,
+                    workflow.out.versions
+                ).match()},
+                { assert workflow.success }
+            )
+        }
+
+    }
+
+}
diff --git a/workflows/nf_aggregate/tests/main.nf.test.snap b/workflows/nf_aggregate/tests/main.nf.test.snap
new file mode 100644
index 0000000..533b724
--- /dev/null
+++ b/workflows/nf_aggregate/tests/main.nf.test.snap
@@ -0,0 +1,33 @@
+{
+    "Parameters: default": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "multiqc_report": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "timestamp": "2023-12-04T10:38:26.10265603"
+    },
+    "Should run without failures": {
+        "content": [
+            [
+                "multiqc_report.html:md5,1c7b0ef50b0e93acf89a58e2384309be"
+            ],
+            [
+                "versions.yml:md5,1294de7c9d8f7ce29bbb3a638ac1d108",
+                "versions.yml:md5,43372d67fa3f029a02cc64a571d88e13"
+            ]
+        ],
+        "timestamp": "2023-12-04T15:19:31.112758226"
+    }
+}
\ No newline at end of file
diff --git a/workflows/nf_aggregate/tests/tags.yml b/workflows/nf_aggregate/tests/tags.yml
new file mode 100644
index 0000000..50048dc
--- /dev/null
+++ b/workflows/nf_aggregate/tests/tags.yml
@@ -0,0 +1,2 @@
+workflows_nf_aggregate:
+  - workflows/nf_aggregate/**

From 0dbc43143752d8d870cb274d21fe444a63d47385 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Mon, 4 Dec 2023 15:36:53 +0000
Subject: [PATCH 16/37] Contains check for variable HTML

---
 workflows/nf_aggregate/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/nf_aggregate/tests/main.nf.test b/workflows/nf_aggregate/tests/main.nf.test
index 9585439..bcee8ce 100644
--- a/workflows/nf_aggregate/tests/main.nf.test
+++ b/workflows/nf_aggregate/tests/main.nf.test
@@ -26,9 +26,9 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert snapshot(
-                    workflow.out.multiqc_report,
                     workflow.out.versions
                 ).match()},
+                { assert path(process.out.multiqc_report.get(0)).getText().contains("nf-core/rnaseq_4Bi5xBK6E2Nbhj") },
                 { assert workflow.success }
             )
         }

From 58ed65517eb1f60c1672a9d0a8fc19203a3f9b00 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Mon, 4 Dec 2023 15:52:56 +0000
Subject: [PATCH 17/37] Switch to contains

---
 workflows/nf_aggregate/tests/main.nf.test      | 2 +-
 workflows/nf_aggregate/tests/main.nf.test.snap | 5 +----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/workflows/nf_aggregate/tests/main.nf.test b/workflows/nf_aggregate/tests/main.nf.test
index bcee8ce..ac5f6d7 100644
--- a/workflows/nf_aggregate/tests/main.nf.test
+++ b/workflows/nf_aggregate/tests/main.nf.test
@@ -28,7 +28,7 @@ nextflow_workflow {
                 { assert snapshot(
                     workflow.out.versions
                 ).match()},
-                { assert path(process.out.multiqc_report.get(0)).getText().contains("nf-core/rnaseq_4Bi5xBK6E2Nbhj") },
+                { assert path(workflow.out.multiqc_report.get(0)).getText().contains("nf-core/rnaseq_4Bi5xBK6E2Nbhj") },
                 { assert workflow.success }
             )
         }
diff --git a/workflows/nf_aggregate/tests/main.nf.test.snap b/workflows/nf_aggregate/tests/main.nf.test.snap
index 533b724..2d875da 100644
--- a/workflows/nf_aggregate/tests/main.nf.test.snap
+++ b/workflows/nf_aggregate/tests/main.nf.test.snap
@@ -20,14 +20,11 @@
     },
     "Should run without failures": {
         "content": [
-            [
-                "multiqc_report.html:md5,1c7b0ef50b0e93acf89a58e2384309be"
-            ],
             [
                 "versions.yml:md5,1294de7c9d8f7ce29bbb3a638ac1d108",
                 "versions.yml:md5,43372d67fa3f029a02cc64a571d88e13"
             ]
         ],
-        "timestamp": "2023-12-04T15:19:31.112758226"
+        "timestamp": "2023-12-04T15:47:00.36029546"
     }
 }
\ No newline at end of file

From ad114437bf15a708e6da3517cb73c14fe9d2479b Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Mon, 4 Dec 2023 17:16:19 +0000
Subject: [PATCH 18/37] Add subworkflow tests

---
 .../utils_nf_aggregate/tests/main.nf.test     | 41 +++++++++++++++++++
 .../tests/main.nf.test.snap                   | 25 +++++++++++
 .../local/utils_nf_aggregate/tests/tags.yml   |  2 +
 3 files changed, 68 insertions(+)
 create mode 100644 subworkflows/local/utils_nf_aggregate/tests/main.nf.test
 create mode 100644 subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap
 create mode 100644 subworkflows/local/utils_nf_aggregate/tests/tags.yml

diff --git a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
new file mode 100644
index 0000000..c2cf408
--- /dev/null
+++ b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
@@ -0,0 +1,41 @@
+nextflow_workflow {
+
+    name "Test Workflow PIPELINE_INITIALISATION"
+    script "../main.nf"
+    workflow "PIPELINE_INITIALISATION"
+
+    tag "subworkflows"
+    tag "subworkflows_local_utils_nf_aggregate"
+    
+    stage {
+        symlink "nextflow_schema.json"
+        symlink "workflows/nf_aggregate/assets/test_run_ids.csv"
+    }
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                // outdir = "tests/results"
+            }
+            workflow {
+                """
+                // define inputs of the workflow here. Example:
+                // input[0] = file("test-file.txt")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.ids
+                 ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap
new file mode 100644
index 0000000..97c8cdf
--- /dev/null
+++ b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap
@@ -0,0 +1,25 @@
+{
+    "Should run without failures": {
+        "content": [
+            [
+                {
+                    "id": "2lXd1j7OwZVfxh",
+                    "workspace": "community/showcase"
+                },
+                {
+                    "id": "38QXz4OfQDpwOV",
+                    "workspace": "community/showcase"
+                },
+                {
+                    "id": "4Bi5xBK6E2Nbhj",
+                    "workspace": "community/showcase"
+                },
+                {
+                    "id": "4LWT4uaXDaGcDY",
+                    "workspace": "community/showcase"
+                }
+            ]
+        ],
+        "timestamp": "2023-12-04T17:13:53.098963"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/local/utils_nf_aggregate/tests/tags.yml b/subworkflows/local/utils_nf_aggregate/tests/tags.yml
new file mode 100644
index 0000000..4fc1520
--- /dev/null
+++ b/subworkflows/local/utils_nf_aggregate/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows_local_utils_nf_aggregate:
+  - subworkflows/local/utils_nf_aggregate/**

From 000be55105c0e6c839e77f6ab147c765b7f6b05e Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Mon, 4 Dec 2023 17:18:16 +0000
Subject: [PATCH 19/37] Remove unused params

---
 subworkflows/local/utils_nf_aggregate/tests/main.nf.test | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
index c2cf408..ecc46f5 100644
--- a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
+++ b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
@@ -15,10 +15,6 @@ nextflow_workflow {
     test("Should run without failures") {
 
         when {
-            params {
-                // define parameters here. Example:
-                // outdir = "tests/results"
-            }
             workflow {
                 """
                 // define inputs of the workflow here. Example:

From 255a6d1b0e6f779356ebe97ef09d7e078e8eeecf Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 11:31:46 +0000
Subject: [PATCH 20/37] Bump to multiqc without fastqc

---
 modules.json                               |  2 +-
 modules/nf-core/multiqc/nextflow.config    | 10 -------
 modules/nf-core/multiqc/tests/main.nf.test | 32 ++--------------------
 3 files changed, 3 insertions(+), 41 deletions(-)
 delete mode 100644 modules/nf-core/multiqc/nextflow.config

diff --git a/modules.json b/modules.json
index 01231a9..d650ecf 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "1537442a7be4a78efa3d1ff700a923c627bbda5d",
+                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config
deleted file mode 100644
index 4e507e7..0000000
--- a/modules/nf-core/multiqc/nextflow.config
+++ /dev/null
@@ -1,10 +0,0 @@
-process {
-    withName: 'MULTIQC' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
-        publishDir = [
-            path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
index 68fffa9..c2dad21 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -9,27 +9,13 @@ nextflow_process {
 
     test("MULTIQC: FASTQC") {
 
-        setup {
-            run("FASTQC") {
-                script "../../fastqc/main.nf"
-                process {
-                """
-                input[0] = Channel.of([
-                    [ id: 'test', single_end: false ],
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-                ])
-                """
-                }
-            }
-        }
-
         when {
             params {
                 outdir = "$outputDir"
             }
             process {
                 """
-                input[0] = FASTQC.out.zip.collect { it[1] }
+                input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
                 input[1] = []
                 input[2] = []
                 input[3] = []
@@ -50,27 +36,13 @@ nextflow_process {
 
     test("MULTIQC: FASTQC and a config file") {
 
-        setup {
-            run("FASTQC") {
-                script "../../fastqc/main.nf"
-                process {
-                """
-                input[0] = Channel.of([
-                    [ id: 'test', single_end: false ],
-                    [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-                ])
-                """
-                }
-            }
-        }
-
         when {
             params {
                 outdir = "$outputDir"
             }
             process {
                 """
-                input[0] = FASTQC.out.zip.collect { it[1] }
+                input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)])
                 input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
                 input[2] = []
                 input[3] = []

From 34c1f753450d298dbc5e3695e1dc902650684ab8 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 11:39:45 +0000
Subject: [PATCH 21/37] Reinstate multiqc config

---
 modules/nf-core/multiqc/nextflow.config | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 modules/nf-core/multiqc/nextflow.config

diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config
new file mode 100644
index 0000000..4e507e7
--- /dev/null
+++ b/modules/nf-core/multiqc/nextflow.config
@@ -0,0 +1,10 @@
+process {
+    withName: 'MULTIQC' {
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}
\ No newline at end of file

From 155c62917b96037b242b54d0f9b956708d430b15 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 11:57:11 +0000
Subject: [PATCH 22/37] Revert "Remove config for test data"

This reverts commit 24751945f63fcf8375b0ad11d65730a6de21f276.
---
 nf-test.config        | 2 +-
 tests/nextflow.config | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)
 create mode 100644 tests/nextflow.config

diff --git a/nf-test.config b/nf-test.config
index 2f5050c..c0ca9e3 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -6,7 +6,7 @@ config {
     workDir ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
-    configFile "nextflow.config"
+    configFile "tests/nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
     profile ""
diff --git a/tests/nextflow.config b/tests/nextflow.config
new file mode 100644
index 0000000..fec66b4
--- /dev/null
+++ b/tests/nextflow.config
@@ -0,0 +1 @@
+includeConfig 'https://raw.githubusercontent.com/nf-core/modules/47ad5f5402a5125c6c6f6107abc9a8732ce7dd12/tests/config/test_data.config'
\ No newline at end of file

From 23c0a057f5b483697ec91b149730170a2dcd9ec8 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 12:03:36 +0000
Subject: [PATCH 23/37] Bump modules sha for test data

---
 tests/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index fec66b4..c6d5e48 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1 +1 @@
-includeConfig 'https://raw.githubusercontent.com/nf-core/modules/47ad5f5402a5125c6c6f6107abc9a8732ce7dd12/tests/config/test_data.config'
\ No newline at end of file
+includeConfig 'https://raw.githubusercontent.com/nf-core/modules/ 0094ae45ba8f5a2e30644d4e252970775a03ee91/tests/config/test_data.config'

From 13e6b4bfc354c4da8ee77f2a7044ba49f438df4d Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 12:04:00 +0000
Subject: [PATCH 24/37] Fix typo

---
 tests/nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index c6d5e48..350286b 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1 +1 @@
-includeConfig 'https://raw.githubusercontent.com/nf-core/modules/ 0094ae45ba8f5a2e30644d4e252970775a03ee91/tests/config/test_data.config'
+includeConfig 'https://raw.githubusercontent.com/nf-core/modules/0094ae45ba8f5a2e30644d4e252970775a03ee91/tests/config/test_data.config'

From 7daa4e88e7b14d4c6fd729b871d933d6ecfb2a9f Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 18:51:11 +0000
Subject: [PATCH 25/37] Try again to bypass the filtering

---
 .github/workflows/ci.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 535b431..8392885 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,8 +23,7 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      # Expose matched filters as job 'tags' output variable
-      tags: ${{ steps.filter.outputs.changes }}
+      tags: ${{ steps.get_tags.outputs.tags }}
     steps:
       - uses: actions/checkout@v3
       - name: Combine all tags.yml files
@@ -32,10 +31,11 @@ jobs:
         run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
       - name: debug
         run: cat .github/tags.yml
-      - uses: dorny/paths-filter@v2
-        id: filter
+      - name: Get tags using yq
+        id: get_tags
+        uses: mikefarah/yq@master
         with:
-          filters: ".github/tags.yml"
+          cmd: 'echo "tags=$(yq -e ". | keys | tojson" .github/tags.yml)" >> $GITHUB_ENV'
 
   nf-test:
     name: nf-test ${{ matrix.tags }} ${{ matrix.profile }}
@@ -50,7 +50,7 @@ jobs:
         NXF_VER:
           - "23.10.0"
           - "latest-everything"
-        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        tags: ${{ fromJson(needs.changes.outputs.tags) }}
         profile:
           - "docker"
 

From 7f87368655d0699203c3aae98a37e00ecdc6b81f Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 19:38:45 +0000
Subject: [PATCH 26/37] Fix env -> out

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8392885..9446895 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -35,7 +35,7 @@ jobs:
         id: get_tags
         uses: mikefarah/yq@master
         with:
-          cmd: 'echo "tags=$(yq -e ". | keys | tojson" .github/tags.yml)" >> $GITHUB_ENV'
+          cmd: 'echo "tags=$(yq -e ". | keys | tojson" .github/tags.yml)" >> $GITHUB_OUTPUT'
 
   nf-test:
     name: nf-test ${{ matrix.tags }} ${{ matrix.profile }}

From 651eda4005a4fedff5cbba7a4724df9eb7753a3d Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 19:45:33 +0000
Subject: [PATCH 27/37] Fix output bit

---
 .github/workflows/ci.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9446895..2d547df 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,8 +34,9 @@ jobs:
       - name: Get tags using yq
         id: get_tags
         uses: mikefarah/yq@master
-        with:
-          cmd: 'echo "tags=$(yq -e ". | keys | tojson" .github/tags.yml)" >> $GITHUB_OUTPUT'
+        run: |
+          tags="$(yq -e '. | keys | tojson' .github/tags.yml)"
+          echo "tags=$tags" >> "$GITHUB_OUTPUT"
 
   nf-test:
     name: nf-test ${{ matrix.tags }} ${{ matrix.profile }}

From 19f42db9f298a10f04ee74c07d2b1a6893f63900 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 19:51:52 +0000
Subject: [PATCH 28/37] fix up yq actions usage

---
 .github/workflows/ci.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2d547df..56c877e 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -23,7 +23,7 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      tags: ${{ steps.get_tags.outputs.tags }}
+      tags: ${{ steps.get_tags.outputs.result }}
     steps:
       - uses: actions/checkout@v3
       - name: Combine all tags.yml files
@@ -34,9 +34,8 @@ jobs:
       - name: Get tags using yq
         id: get_tags
         uses: mikefarah/yq@master
-        run: |
-          tags="$(yq -e '. | keys | tojson' .github/tags.yml)"
-          echo "tags=$tags" >> "$GITHUB_OUTPUT"
+        with:
+          cmd: yq -e '. | keys | tojson' .github/tags.yml
 
   nf-test:
     name: nf-test ${{ matrix.tags }} ${{ matrix.profile }}

From ec14aa0e3f81695a5e0ef4940a813522b4d5ee1b Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 5 Dec 2023 20:13:23 +0000
Subject: [PATCH 29/37] Tweaks

---
 .github/workflows/ci.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 56c877e..07952f2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ concurrency:
 
 jobs:
   changes:
-    name: Check for changes
+    name: Find tags to test
     runs-on: ubuntu-latest
     outputs:
       tags: ${{ steps.get_tags.outputs.result }}
@@ -38,7 +38,7 @@ jobs:
           cmd: yq -e '. | keys | tojson' .github/tags.yml
 
   nf-test:
-    name: nf-test ${{ matrix.tags }} ${{ matrix.profile }}
+    name: nf-test ${{ matrix.tags }} ${{ matrix.profile }} nf-${{ matrix.NXF_VER }}
     needs: [changes]
     if: needs.changes.outputs.tags != '[]'
     runs-on: ubuntu-latest
@@ -80,7 +80,7 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml --verbose
 
       - name: Output log on failure
         if: failure()

From dec50d59e33bee1e311990a465fd2b0db014bc4d Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 6 Dec 2023 10:52:06 +0000
Subject: [PATCH 30/37] Remove reports from nf-test configuration

---
 tests/nextflow.config | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/nextflow.config b/tests/nextflow.config
index 350286b..fc1e56c 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -1 +1,6 @@
 includeConfig 'https://raw.githubusercontent.com/nf-core/modules/0094ae45ba8f5a2e30644d4e252970775a03ee91/tests/config/test_data.config'
+
+timeline.enabled = false
+report.enabled   = false
+trace.enabled    = false
+dag.enabled      = false
\ No newline at end of file

From 68ccda2728db5bfaa236e9fc5b7234d0bf19c0a0 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 6 Dec 2023 11:50:02 +0000
Subject: [PATCH 31/37] Remove params from nf-aggregate workflow

---
 main.nf                                   | 5 ++++-
 workflows/nf_aggregate/main.nf            | 9 ++++++---
 workflows/nf_aggregate/tests/main.nf.test | 3 +++
 3 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index 003d43f..b979634 100644
--- a/main.nf
+++ b/main.nf
@@ -43,7 +43,10 @@ workflow {
     NF_AGGREGATE (
         PIPELINE_INITIALISATION.out.ids,
         ch_multiqc_custom_config,
-        ch_multiqc_logo
+        ch_multiqc_logo,
+        params.seqera_api_endpoint,
+        params.skip_run_gantt,
+        params.skip_multiqc
     )
 }
 
diff --git a/workflows/nf_aggregate/main.nf b/workflows/nf_aggregate/main.nf
index 9658be4..8208174 100644
--- a/workflows/nf_aggregate/main.nf
+++ b/workflows/nf_aggregate/main.nf
@@ -16,6 +16,9 @@ workflow NF_AGGREGATE {
     ids                   // channel: run ids read in from --input
     multiqc_custom_config // channel: user specified custom config file used by MultiQC
     multiqc_logo          // channel: logo rendered in MultiQC report
+    seqera_api_endpoint   //     val: Seqera Platform API endpoint URL
+    skip_run_gantt        //     val: Skip GANTT chart creation for each run
+    skip_multiqc          //     val: Skip MultiQC
 
     main:
 
@@ -27,14 +30,14 @@ workflow NF_AGGREGATE {
     //
     SEQERA_RUNS_DUMP (
         ids,
-        params.seqera_api_endpoint
+        seqera_api_endpoint
     )
     ch_versions = ch_versions.mix(SEQERA_RUNS_DUMP.out.versions.first())
 
     //
     // MODULE: Generate Gantt chart for workflow execution
     //
-    if (!params.skip_run_gantt) {
+    if (!skip_run_gantt) {
         PLOT_RUN_GANTT (
             SEQERA_RUNS_DUMP.out.run_dump
         )
@@ -55,7 +58,7 @@ workflow NF_AGGREGATE {
     // MODULE: MultiQC
     //
     ch_multiqc_report = Channel.empty()
-    if (!params.skip_multiqc) {
+    if (!skip_multiqc) {
         ch_multiqc_config = Channel.fromPath("$projectDir/workflows/nf_aggregate/assets/multiqc_config.yml", checkIfExists: true)
         summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
         ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
diff --git a/workflows/nf_aggregate/tests/main.nf.test b/workflows/nf_aggregate/tests/main.nf.test
index ac5f6d7..1243975 100644
--- a/workflows/nf_aggregate/tests/main.nf.test
+++ b/workflows/nf_aggregate/tests/main.nf.test
@@ -19,6 +19,9 @@ nextflow_workflow {
                 input[0] = ['id': '4Bi5xBK6E2Nbhj', 'workspace': 'community/showcase']
                 input[1] = []
                 input[2] = []
+                input[3] = 'https://api.tower.nf'
+                input[4] = false
+                input[5] = false
                 """
             }
         }

From d5cd84899ac19b36740f8e54dce8d9033ede3db7 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 6 Dec 2023 11:53:21 +0000
Subject: [PATCH 32/37] Remove explicit params.publish_dir_mode definition in
 tests

---
 modules/local/plot_run_gantt/tests/main.nf.test   | 4 ----
 modules/local/seqera_runs_dump/tests/main.nf.test | 3 ---
 2 files changed, 7 deletions(-)

diff --git a/modules/local/plot_run_gantt/tests/main.nf.test b/modules/local/plot_run_gantt/tests/main.nf.test
index bacc703..712ed7c 100644
--- a/modules/local/plot_run_gantt/tests/main.nf.test
+++ b/modules/local/plot_run_gantt/tests/main.nf.test
@@ -23,11 +23,7 @@ nextflow_process {
         }
 
         when {
-            params {
-                publish_dir_mode = "copy"
-            }
             process {
-
                 """
                 input[0] = SEQERA_RUNS_DUMP.out.run_dump
                 """
diff --git a/modules/local/seqera_runs_dump/tests/main.nf.test b/modules/local/seqera_runs_dump/tests/main.nf.test
index ccce4ce..9d90498 100644
--- a/modules/local/seqera_runs_dump/tests/main.nf.test
+++ b/modules/local/seqera_runs_dump/tests/main.nf.test
@@ -11,9 +11,6 @@ nextflow_process {
     test("Should run without failures") {
 
         when {
-            params {
-                publish_dir_mode = "copy"
-            }
             process {
                 """
                 input[0] = ['id': '4Bi5xBK6E2Nbhj', 'workspace': 'community/showcase']

From d9521fa1f4c743f92e9643ab8b01f5f232167c81 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 6 Dec 2023 12:05:40 +0000
Subject: [PATCH 33/37] Update UTILS_NFVALIDATION_PLUGIN subworkflow

---
 modules.json                                              | 2 +-
 .../nf-core/utils_nfvalidation_plugin/tests/main.nf.test  | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/modules.json b/modules.json
index d650ecf..eecf5c4 100644
--- a/modules.json
+++ b/modules.json
@@ -21,7 +21,7 @@
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
-                        "git_sha": "c81784b47d44464b35e04220e00051bb5be27524",
+                        "git_sha": "f0f8f4dc889970251eb251b85610f7ec2eafded9",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
index f95b967..904f97b 100644
--- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
+++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
@@ -3,8 +3,10 @@ nextflow_workflow {
     name "Test Workflow UTILS_NFVALIDATION_PLUGIN"
     script "../main.nf"
     workflow "UTILS_NFVALIDATION_PLUGIN"
-    tag "subworkflow"
-    tag "subworkflow_nfcore"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "plugin/nf-validation"
+    tag "'plugin/nf-validation'"
     tag "utils_nfvalidation_plugin"
     tag "subworkflows/utils_nfvalidation_plugin"
 
@@ -168,6 +170,7 @@ nextflow_workflow {
             params {
                 monochrome_logs = true
                 test_data       = ''
+                outdir          = 1
             }
             workflow {
                 """
@@ -191,7 +194,6 @@ nextflow_workflow {
         then {
             assert workflow.failed
             assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') }
-            assert workflow.stdout.any { it.contains('The following invalid input values have been detected:') }
         }
 
     }

From 64fb120a8b04f68171935bef000a028e31606ddf Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Wed, 6 Dec 2023 12:20:26 +0000
Subject: [PATCH 34/37] Add final CI test to confirm all nf-tests passed

---
 .github/workflows/ci.yml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 07952f2..faa0742 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -93,3 +93,21 @@ jobs:
         if: always() # always run even if the previous step fails
         with:
           report_paths: test.xml
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs: [changes, nf-test]
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

From 20d8a3a76ce2d49886e0f31847f6fd744ffa666b Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Wed, 6 Dec 2023 15:55:34 +0000
Subject: [PATCH 35/37] Try workdir thing

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
---
 nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf-test.config b/nf-test.config
index c0ca9e3..0a4311a 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir ".nf-test"
+    workDir { System.getenv("TMPDIR") ?: '.nf-test' }
 
     // location of an optional nextflow.config file specific for executing tests
     configFile "tests/nextflow.config"

From 520fd129f8a6de071e0ee36ffe19b898c96a5693 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Wed, 6 Dec 2023 15:59:00 +0000
Subject: [PATCH 36/37] try tmpdir thing without closure

---
 nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf-test.config b/nf-test.config
index 0a4311a..c7fed01 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -3,7 +3,7 @@ config {
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir { System.getenv("TMPDIR") ?: '.nf-test' }
+    workDir System.getenv("TMPDIR") ?: '.nf-test'
 
     // location of an optional nextflow.config file specific for executing tests
     configFile "tests/nextflow.config"

From 9af0c7eebf25e99aaf59dad390db87df82f6f830 Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Wed, 6 Dec 2023 16:22:14 +0000
Subject: [PATCH 37/37] Ignore process selector warnings by default in favour
 of using -profile debug

---
 nextflow.config | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index b148b09..a14bc20 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -51,16 +51,13 @@ process {
     maxErrors     = '-1'
 }
 
+// Ignore process selector warnings by default
+nextflow.enable.configProcessNamesValidation = false
+
 profiles {
     test { 
         params.input = "${projectDir}/workflows/nf_aggregate/assets/test_run_ids.csv"
     }
-    wave {
-        wave.enabled = true
-        wave.strategy = ['conda', 'container', 'dockerfile', 'spack']
-        wave.build.repository = 'quay.io/seqeralabs/nf-aggregate'
-        wave.freeze = true   
-    }
     test_full {
         params.input = "${projectDir}/workflows/nf_aggregate/assets/test_run_ids.csv"
     }
@@ -68,6 +65,13 @@ profiles {
         dumpHashes             = true
         process.beforeScript   = 'echo $HOSTNAME'
         cleanup                = false
+        nextflow.enable.configProcessNamesValidation = true
+    }
+    wave {
+        wave.enabled = true
+        wave.strategy = ['conda', 'container', 'dockerfile', 'spack']
+        wave.build.repository = 'quay.io/seqeralabs/nf-aggregate'
+        wave.freeze = true   
     }
     conda {
         conda.enabled          = true