Merge pull request #248 from nf-core/release_pr_comments

Removed customdumpsoftwareversions and updated README.md
nf-core · Aug 13, 2024 · 7b37e90 · 7b37e90
2 parents ee35363 + b48fba9
commit 7b37e90
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diff --git a/README.md b/README.md
@@ -33,7 +33,8 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Pipeline summary
 
-1. Demultiplexing
+1. [samshee](#samshee) - Validates illumina v2 samplesheets.
+2. Demultiplexing
 
 - [bcl-convert](#bcl-convert) - converting bcl files to fastq, and demultiplexing (CONDITIONAL)
 - [bases2fastq](#bases2fastq) - converting bases files to fastq, and demultiplexing (CONDITIONAL)
@@ -42,12 +43,11 @@ On release, automated continuous integration tests run the pipeline on a full-si
 - [fqtk](#fqtk) - a toolkit for working with FASTQ files, written in Rust (CONDITIONAL)
 - [mkfastq](#mkfastq) - converting bcl files to fastq, and demultiplexing for single-cell sequencing data (CONDITIONAL)
 
-2. [checkqc](#checkqc) - (optional) Check quality criteria after demultiplexing (bcl2fastq only)
-3. [fastp](#fastp) - Adapter and quality trimming
-4. [Falco](#falco) - Raw read QC
-5. [md5sum](#md5sum) - Creates an MD5 (128-bit) checksum of every fastq.
-6. [MultiQC](#multiqc) - aggregate report, describing results of the whole pipeline
-7. [samshee](#samshee) - Validates illumina v2 samplesheets.
+3. [checkqc](#checkqc) - (optional) Check quality criteria after demultiplexing (bcl2fastq only)
+4. [fastp](#fastp) - Adapter and quality trimming
+5. [Falco](#falco) - Raw read QC
+6. [md5sum](#md5sum) - Creates an MD5 (128-bit) checksum of every fastq.
+7. [MultiQC](#multiqc) - aggregate report, describing results of the whole pipeline
 
 ![subway map](docs/demultiplex.png)
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -158,14 +158,6 @@ process {
         ]
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
     withName: SGDEMUX {
         publishDir = [
             [

diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml