Added TrimGalore

.github/workflows/fastqc.yml

@@ -1,3 +1,4 @@
+name: FastQC
 on:
   push:
     paths: tools/fastqc/*
@@ -14,5 +15,4 @@ jobs:
     - uses: actions/checkout@v1
 
     # Test the module
-    - name: FastQC
-      run: nextflow run ./tools/fastqc/test/
+    - run: nextflow run ./tools/fastqc/test/

.github/workflows/samtools_index.yml

@@ -1,8 +1,9 @@
+name: samtools index
 on:
   push:
-    paths: tools/samtools/sort*
+    paths: tools/samtools/index*
   pull_request:
-    paths: tools/samtools/sort*
+    paths: tools/samtools/index*
 
 jobs:
   run_multiqc:
@@ -14,5 +15,4 @@ jobs:
     - uses: actions/checkout@v1
 
     # Test the module
-    - name: samtools sort
-      run: nextflow run ./tools/samtools/sort/test/
+    - run: nextflow run ./tools/samtools/index/test/

.github/workflows/samtools_sort.yml

@@ -1,8 +1,9 @@
+name: samtools sort
 on:
   push:
-    paths: tools/samtools/index*
+    paths: tools/samtools/sort*
   pull_request:
-    paths: tools/samtools/index*
+    paths: tools/samtools/sort*
 
 jobs:
   run_multiqc:
@@ -14,5 +15,4 @@ jobs:
     - uses: actions/checkout@v1
 
     # Test the module
-    - name: samtools index
-      run: nextflow run ./tools/samtools/index/test/
+    - run: nextflow run ./tools/samtools/sort/test/

.github/workflows/trim_galore.yml

@@ -0,0 +1,18 @@
+name: Trim Galore!
+on:
+  push:
+    paths: tools/trim_galore/*
+  pull_request:
+    paths: tools/trim_galore/*
+
+jobs:
+  run_multiqc:
+    runs-on: ubuntu-latest
+
+    steps:
+
+    # Check out the repository
+    - uses: actions/checkout@v1
+
+    # Test the module
+    - run: nextflow run ./tools/trim_galore/test/

tools/fastqc/main.nf

@@ -3,7 +3,7 @@ process fastqc {
     publishDir "${params.outdir}/fastqc", mode: 'copy',
         saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
 
-        container: 'quay.io/biocontainers/fastqc:0.11.8--2'
+    container: 'quay.io/biocontainers/fastqc:0.11.8--2'
 
     input:
     set val(sample_id), file(reads)

tools/trim_galore/main.nf

@@ -0,0 +1,35 @@
+process fastqc {
+    tag "$sample_id"
+    publishDir "${params.outdir}/trim_galore", mode: 'copy',
+        saveAs: {filename ->
+            if (filename.indexOf("_fastqc") > 0) "FastQC/$filename"
+            else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
+            else filename
+        }
+
+    container: 'quay.io/biocontainers/trim-galore:0.6.5--0'
+
+    input:
+    set val(sample_id), file(reads)
+
+    output:
+    set val(name), file("*fq.gz")
+    file "*trimming_report.txt"
+    file "*_fastqc.{zip,html}"
+
+    script:
+    c_r1 = clip_r1 > 0 ? "--clip_r1 ${clip_r1}" : ''
+    c_r2 = clip_r2 > 0 ? "--clip_r2 ${clip_r2}" : ''
+    tpc_r1 = three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${three_prime_clip_r1}" : ''
+    tpc_r2 = three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${three_prime_clip_r2}" : ''
+    nextseq = params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : ''
+    if (params.singleEnd) {
+        """
+        trim_galore --fastqc --gzip $c_r1 $tpc_r1 $nextseq $reads
+        """
+    } else {
+        """
+        trim_galore --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq $reads
+        """
+    }
+}

tools/trim_galore/meta.yml

@@ -0,0 +1,43 @@
+name: Trim Galore!
+description: Trim FastQ files using Trim Galore!
+keywords:
+    - trimming
+    - adapters
+    - sequencing adapters
+tools:
+    - fastqc:
+        description: |
+            A wrapper tool around Cutadapt and FastQC to consistently apply quality
+            and adapter trimming to FastQ files, with some extra functionality for
+            MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
+        homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
+        documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
+input:
+    -
+        - sample_id:
+            type: string
+            description: Sample identifier
+        - reads:
+            type: file
+            description: Input FastQ file, or pair of files
+output:
+    -
+        - sample_id:
+            type: string
+            description: Sample identifier
+        - trimmed_fastq:
+            type: file
+            description: Trimmed FastQ files
+            pattern: *fq.gz
+    -
+        - report:
+            type: file
+            description: Trim Galore! trimming report
+            pattern: *trimming_report.txt
+    -
+        - fastqc_report:
+            type: file
+            description: FastQC report
+            pattern: *_fastqc.{zip,html}
+authors:
+    - @ewels

tools/trim_galore/test/main.nf

@@ -0,0 +1 @@
+/* A mini pipeline to test FastQC here */