Update docs for trimgalore

software/trimgalore/meta.yml

@@ -1,40 +1,98 @@
-name: Trim Galore!
+name: trimgalore
 description: Trim FastQ files using Trim Galore!
 keywords:
-    - trimming
+  - trimming
-    - adapters
+  - adapters
-    - sequencing adapters
+  - sequencing adapters
 tools:
-    - fastqc:
+  - trimgalore:
-        description: |
+      description: |
-            A wrapper tool around Cutadapt and FastQC to consistently apply quality
+        A wrapper tool around Cutadapt and FastQC to consistently apply quality
-            and adapter trimming to FastQ files, with some extra functionality for
+        and adapter trimming to FastQ files, with some extra functionality for
-            MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
+        MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
-        homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
+      homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
-        documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
+      documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+  - clip_r1:
+      type: integer
+      description: |
+        Instructs Trim Galore to remove bp from the 5' end of read 1
+        (or single-end reads)
+  - clip_r2:
+      type: integer
+      description: |
+        Instructs Trim Galore to remove bp from the 5' end of read 2
+        (paired-end reads only)
+  - three_prime_clip_r1:
+      type: integer
+      description: |
+        Instructs Trim Galore to remove bp from the 3' end of read 1
+        AFTER adapter/quality trimming has been performed
+  - three_prime_clip_r2:
+      type: integer
+      description: |
+        Instructs Trim Galore to re move bp from the 3' end of read 2
+        AFTER adapter/quality trimming has been performed
 input:
-    -
+  - meta:
-        - sample_id:
+      type: map
-            type: string
+      description: |
-            description: Sample identifier
+        Groovy Map containing sample information
-        - reads:
+        e.g. [ id:'test', single_end:false ]
-            type: file
+  - reads:
-            description: Input FastQ file, or pair of files
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - options:
+      type: map
+      description: |
+        Groovy Map containing module options for passing command-line arguments and
+        output file paths.
 output:
-    -
+  - meta:
-        - sample_id:
+      type: map
-            type: string
+      description: |
-            description: Sample identifier
+        Groovy Map containing sample information
-        - trimmed_fastq:
+        e.g. [ id:'test', single_end:false ]
-            type: file
+  - reads:
-            description: Trimmed FastQ files
+      type: file
-            pattern: "*fq.gz"
+      description: |
-    -
+        List of input adapter trimmed FastQ files of size 1 and 2 for
-        - report:
+        single-end and paired-end data, respectively.
-            type: file
+      pattern: "*.fq.gz"
-            description: Trim Galore! trimming report
+  - html:
-            pattern: "*trimming_report.txt"
+      type: file
-
+      description: FastQC report (optional)
+      pattern: "*_fastqc.html"
+  - zip:
+      type: file
+      description: FastQC report archive (optional)
+      pattern: "*_fastqc.zip"
+  - log:
+      type: file
+      description: Trim Galore! trimming report
+      pattern: "*report.txt"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
 authors:
+    - "@drpatelh"
     - "@ewels"
     - "@FelixKrueger"