From 121e9df1cb1d1c7ec1ca1fd8567830762e2f4d6f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 2 Oct 2023 17:56:26 +0200 Subject: [PATCH 1/5] change default input samplesheet to test one insead of fake file as nf-validation now checks file existence --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index a81e3ea2..2b3c3497 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,7 +10,7 @@ params { // Input options - input = "fake_input_to_build_refs.csv" + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' // a valid samplesheet has to be present for parameter validation when building references build_references = false cosmic_username = null cosmic_passwd = null From 897a544c58992c5fa295ae945ba54374efccd0b6 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 18 Oct 2023 12:48:12 +0200 Subject: [PATCH 2/5] make input existence not mendatory, so building references does not require one --- nextflow.config | 2 +- nextflow_schema.json | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 2b3c3497..a81e3ea2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,7 +10,7 @@ params { // Input options - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' // a valid samplesheet has to be present for parameter validation when building references + input = "fake_input_to_build_refs.csv" build_references = false cosmic_username = null cosmic_passwd = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 611da821..1c8962f9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -32,7 +32,6 @@ "input": { "type": "string", "format": "file-path", - "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", "description": "Path to comma-separated file containing information about the samples in the experiment.", From b21b4aae4f627e368f3fe98287bc6557976dadbf Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 18 Oct 2023 13:39:14 +0200 Subject: [PATCH 3/5] add publishing directory for convert2bed files --- conf/modules.config | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 3e0afe44..9a218711 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -45,6 +45,14 @@ process { ] } + withName: CONVERT2BED { + publishDir = [ + path: { "${params.genomes_base}/convert2bed" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, @@ -178,11 +186,6 @@ process { ext.when = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)} } - withName: REFORMAT { - ext.args = "forcetrimright=75" - ext.args2 = "forcetrimleft=75" - } - withName: SAMPLESHEET_CHECK { publishDir = [ path: { "${params.outdir}/pipeline_info" }, From 81118ed1688b3566417e1a9df990edda836c202f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 18 Oct 2023 17:10:33 +0200 Subject: [PATCH 4/5] update fusionreport --- modules/local/fusionreport/detect/main.nf | 2 +- modules/local/fusionreport/download/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 9605d8a8..b398ef7b 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -4,7 +4,7 @@ process FUSIONREPORT { // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p4" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p5" input: diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index 3ab1bc03..e18955cc 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -4,7 +4,7 @@ process FUSIONREPORT_DOWNLOAD { // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p4" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p5" input: val(username) From fffb37b00328cdf3e5451f093daa0bb06f36a328 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 20 Oct 2023 10:28:40 +0200 Subject: [PATCH 5/5] update changelog --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 66a4ecd1..d67a99d5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,10 +10,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389) +- Now publishing convert2bed output to convert2bed to keep the output file for mosdepth [#420](https://github.com/nf-core/rnafusion/pull/420) +- No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420) ### Fixed - Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416) +- Updated COSMIC database to fix 404 error while downloading fusionreport references [#420](https://github.com/nf-core/rnafusion/pull/420) ### Removed