Merge pull request #287 from JoseEspinosa/more_fixes

More/last fixes before 2.0 release
nf-core · Jul 22, 2022 · 9582d07 · 9582d07
2 parents 5f3020f + fa733cc
commit 9582d07
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [nf-core/tools#1415](https://github.com/nf-core/tools/issues/1415) - Make `--outdir` a mandatory parameter
 - [[282](https://github.com/nf-core/chipseq/issues/282)] - Fix `genome.fa` publication for IGV.
 - [[280](https://github.com/nf-core/chipseq/issues/280)] - Update `macs_gsize` in `igenomes.config`, create a new `--read_length` parameter and implement the logic to calculate `--macs_gsize` when the parameter is missing.
+- Eliminate `if`s conditions from `deseq2_qc` and `macs2_consensus` {local module and use `ext.when` instead.
+- Remove `deseq2` differential binding analysis of consensus peaks.
 
 ### Parameters
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -65,6 +65,15 @@ process {
         ]
     }
 
+    withName: 'UNTAR_CHROMAP_INDEX|CHROMAP_INDEX' {
+        publishDir = [
+            path: { "${params.outdir}/genome/index/chromap" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference
+        ]
+    }
+
     withName: 'GFFREAD' {
         ext.args   = '--keep-exon-attrs -F -T'
         publishDir = [
@@ -88,17 +97,15 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'GENOME_BLACKLIST_REGIONS' {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 }
@@ -162,29 +169,32 @@ if (!params.skip_trimming) {
 }
 
 process {
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
         ext.prefix = { "${meta.id}.Lb.sorted" }
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/samtools" },
-            mode: params.publish_dir_mode
+            path: { "${params.outdir}/${params.aligner}/library" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_align_intermeds
         ]
     }
 
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
-        ext.prefix = { "${meta.id}.Lb.sorted" }
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/samtools" },
+            path: { "${params.outdir}/${params.aligner}/library" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_align_intermeds
         ]
     }
 
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_.*' {
-        ext.prefix = { "${meta.id}.Lb.sorted" }
+    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_.*:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_.*' {
+        ext.prefix = { "${meta.id}.Lb.sorted.bam" }
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/library/samtools_stats" },
+            path: { "${params.outdir}/${params.aligner}/library/samtools_stats/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_align_intermeds
         ]
     }
 }
@@ -202,7 +212,8 @@ if (params.aligner == 'bwa') {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/library" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                enabled: false
             ]
         }
     }
@@ -214,15 +225,23 @@ if (params.aligner == 'bowtie2') {
             ext.args   = ''
             ext.prefix = { "${meta.id}.Lb" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/library" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                [
+                    path: { "${params.outdir}/${params.aligner}/library" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                    enabled: false
+                ],
+                [
+                    path: { "${params.outdir}/${params.aligner}/library/unmapped" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*.fastq.gz',
+                    enabled: params.save_unaligned
+                ]
             ]
         }
     }
 }
 
-
 if (params.aligner == 'chromap') {
     process {
         withName: CHROMAP_INDEX {
@@ -239,7 +258,8 @@ if (params.aligner == 'chromap') {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/library" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+                enabled: false
             ]
         }
     }
@@ -260,17 +280,18 @@ if (params.aligner == 'star') {
             ].join(' ').trim()
             publishDir = [
                 [
-                    path: { "${params.outdir}/${params.aligner}/log" },
+                    path: { "${params.outdir}/${params.aligner}/library/log" },
                     mode: params.publish_dir_mode,
                     pattern: '*.{out,tab}'
                 ],
                 [
                     path: { "${params.outdir}/${params.aligner}/library" },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
+                    enabled: false
                 ],
                 [
-                    path: { "${params.outdir}/${params.aligner}/unmapped" },
+                    path: { "${params.outdir}/${params.aligner}/library/unmapped" },
                     mode: params.publish_dir_mode,
                     pattern: '*.fastq.gz',
                     enabled: params.save_unaligned
@@ -284,11 +305,7 @@ process {
     withName: 'PICARD_MERGESAMFILES' {
         ext.args   = '--SORT_ORDER coordinate --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
         ext.prefix = { "${meta.id}.mLb.sorted" }
-        publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        publishDir = [ enabled: false ]
     }
 
     withName: '.*:MARK_DUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
@@ -313,44 +330,43 @@ process {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
             mode: params.publish_dir_mode,
-            pattern: '*.{bai,csi}'
+            pattern: '*.{bai,csi}',
+            enabled: params.save_align_intermeds
         ]
     }
 
     withName: '.*:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
+        ext.prefix = { "${meta.id}.mLb.mkD.sorted.bam" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary/samtools_stats" },
             mode: params.publish_dir_mode,
             pattern: '*.{stats,flagstat,idxstats}'
         ]
     }
 
+    // Should only be published when paired end data is used and save_align_intermeds is true
     withName: 'BAM_FILTER' {
-        ext.prefix = { "${meta.id}.mLb.flT.sorted" }
+        ext.prefix = { meta.single_end ?  "${meta.id}.mLb.noPublish" : "${meta.id}.mLb.flT.sorted" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            pattern: '*.mLb.flT.sorted.bam',
             enabled: params.save_align_intermeds
         ]
     }
 
     withName: 'BAM_REMOVE_ORPHANS' {
         ext.args   = '--only_fr_pairs'
         ext.prefix = { "${meta.id}.mLb.clN" }
-        publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        publishDir = [ enabled: false ]
     }
 
     withName: 'NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' {
         ext.prefix = { "${meta.id}.mLb.clN.sorted" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
             mode: params.publish_dir_mode,
-            pattern: '*.{bai,csi}'
+            pattern: '*.bam'
         ]
     }
 
@@ -359,12 +375,12 @@ process {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
             mode: params.publish_dir_mode,
-            pattern: "*.bam"
+            pattern: '*.{bai,csi}'
         ]
     }
 
     withName: 'NFCORE_CHIPSEQ:CHIPSEQ:FILTER_BAM_BAMTOOLS:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
-        ext.prefix = { "${meta.id}.mLb.clN.sorted" }
+        ext.prefix = { "${meta.id}.mLb.clN.sorted.bam" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary/samtools_stats" },
             mode: params.publish_dir_mode,
@@ -391,29 +407,20 @@ process {
     }
 
     withName: 'BEDTOOLS_GENOMECOV' {
-        ext.prefix = { "${meta.id}.mLb.clN" }
+        ext.prefix = { "${meta.id}" }
         publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/mergedLibrary/bigwig" },
-                mode: params.publish_dir_mode,
-                pattern: "*.bigWig"
-            ],
-            [
-                path: { "${params.outdir}/${params.aligner}/mergedLibrary/bigwig/scale" },
-                mode: params.publish_dir_mode,
-                pattern: "*.txt"
-            ]
+            path: { "${params.outdir}/${params.aligner}/mergedLibrary/bigwig/scale" },
+            mode: params.publish_dir_mode,
+            pattern: "*.txt"
         ]
     }
 
     withName: 'UCSC_BEDGRAPHTOBIGWIG' {
-        ext.prefix = { "${meta.id}.mLb.clN" }
+        ext.prefix = { "${meta.id}" }
         publishDir = [
-            [
-                path: { "${params.outdir}/${params.aligner}/mergedLibrary/bigwig" },
-                mode: params.publish_dir_mode,
-                pattern: "*.bigWig"
-            ]
+            path: { "${params.outdir}/${params.aligner}/mergedLibrary/bigwig" },
+            mode: params.publish_dir_mode,
+            pattern: "*.bigWig"
         ]
     }
 }
@@ -485,6 +492,12 @@ if (!params.skip_plot_profile) {
     }
 }
 
+process {
+    withName: 'KHMER_UNIQUEKMERS' {
+        publishDir = [ enabled: false ]
+    }
+}
+
 if (!params.skip_plot_fingerprint) {
     process {
         withName: 'DEEPTOOLS_PLOTFINGERPRINT' {
@@ -603,7 +616,8 @@ if (!params.skip_consensus_peaks) {
                 path: { [
                     "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
                     params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                    '/consensus'
+                    '/consensus',
+                    "/${meta.id}"
                     ].join('') },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
@@ -616,7 +630,8 @@ if (!params.skip_consensus_peaks) {
                 path: { [
                     "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
                     params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                    '/consensus'
+                    '/consensus',
+                    "/${meta.id}"
                     ].join('') },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
@@ -633,7 +648,8 @@ if (!params.skip_consensus_peaks) {
                     path: { [
                         "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
                         params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                        '/consensus'
+                        '/consensus',
+                        "/${meta.id}"
                         ].join('') },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
@@ -645,6 +661,7 @@ if (!params.skip_consensus_peaks) {
     if (!params.skip_deseq2_qc) {
         process {
             withName: DESEQ2_QC {
+                ext.when   = { meta.multiple_groups && meta.replicates_exist }
                 ext.args   = [
                     '--id_col 1',
                     '--sample_suffix \'.mLb.clN.sorted.bam\'',
@@ -655,27 +672,29 @@ if (!params.skip_consensus_peaks) {
                     path: { [
                         "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
                         params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                        '/consensus/deseq2'
+                        '/consensus',
+                        "/${meta.id}",
+                        '/deseq2'
                         ].join('') },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
             }
         }
     }
+}
 
-    if (!params.skip_igv) {
-        process {
-            withName: 'IGV' {
-                publishDir = [
-                        path: { [
-                            "${params.outdir}/igv",
-                            params.narrow_peak? '/narrowPeak' : '/broadPeak'
-                            ].join('') },
-                        mode: params.publish_dir_mode,
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
+if (!params.skip_igv) {
+    process {
+        withName: 'IGV' {
+            publishDir = [
+                    path: { [
+                        "${params.outdir}/igv",
+                        params.narrow_peak? '/narrowPeak' : '/broadPeak'
+                        ].join('') },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
         }
     }
 }

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -17,6 +17,9 @@ params {
     // Input data for full size test
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/chipseq/samplesheet/v2.0/samplesheet_full.csv'
 
+    // Used to get macs_gsize
+    read_length = 50
+
     // Genome references
     genome = 'hg19'
 }
diff --git a/docs/images/r_deseq2_ma_plot.png b/docs/images/r_deseq2_ma_plot.png
diff --git a/docs/images/r_deseq2_volcano_plot.png b/docs/images/r_deseq2_volcano_plot.png