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Remove --tracedir #964

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merged 1 commit into from
Mar 17, 2023
Merged

Remove --tracedir #964

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10 changes: 10 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#961](https://github.com/nf-core/rnaseq/pull/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
- Remove HISAT2 from automated AWS full-sized tests

### Parameters

| Old parameter | New parameter |
| ------------- | ------------- |
| `--tracedir` | |

> **NB:** Parameter has been **updated** if both old and new parameter information is present.
> **NB:** Parameter has been **added** if just the new parameter information is present.
> **NB:** Parameter has been **removed** if new parameter information isn't present.

### Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
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9 changes: 4 additions & 5 deletions nextflow.config
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Expand Up @@ -98,7 +98,6 @@ params {

// Boilerplate options
outdir = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
Expand Down Expand Up @@ -233,19 +232,19 @@ env {
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}

manifest {
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7 changes: 0 additions & 7 deletions nextflow_schema.json
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Expand Up @@ -704,13 +704,6 @@
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${params.outdir}/pipeline_info",
"fa_icon": "fas fa-cogs",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
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