Merge pull request #768 from nf-core/adapter-list

Add AR adapterList removal

Author: jfy133

.github/workflows/ci.yml

@@ -102,6 +102,12 @@ jobs:
       - name: ADAPTERREMOVAL Run the basic pipeline with preserve5p end and merged reads only options
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --preserve5p --mergedonly
+      - name: ADAPTER LIST Run the basic pipeline using an adapter list
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt'
+      - name: ADAPTER LIST Run the basic pipeline using an adapter list, skipping adapter removal
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --clip_adapters_list 'https://github.com/nf-core/test-datasets/raw/eager/databases/adapters/adapter-list.txt' --skip_adapterremoval 
       - name: MAPPER_CIRCULARMAPPER Test running with CircularMapper
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --mapper 'circularmapper' --circulartarget 'NC_007596.2'

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
+- [#651](https://github.com/nf-core/eager/issues/651) - Adds removal of adapters specified in an AdapterRemoval adapter list file
+
 ### `Fixed`
 
 - [#771](https://github.com/nf-core/eager/issues/771) Remove legacy code

main.nf

@@ -227,6 +227,20 @@ if( params.bt2_index && params.mapper == 'bowtie2' ){
     bwa_index_bwamem = Channel.empty()
 }
 
+// Adapter removal adapter-list setup
+if ( !params.clip_adapters_list ) {
+    Channel
+      .fromPath("$projectDir/assets/nf-core_eager_dummy2.txt", checkIfExists: true)
+      .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
+      .into {ch_adapterlist}
+} else {
+    Channel
+      .fromPath("${params.clip_adapters_list}", checkIfExists: true)
+      .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
+      .into {ch_adapterlist}
+}
+
+
 // SexDetermination channel set up and bedfile validation
 if (!params.sexdeterrmine_bedfile) {
   ch_bed_for_sexdeterrmine = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
@@ -765,25 +779,27 @@ process adapter_removal {
 
     input:
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file(r1), file(r2) from ch_fastp_for_adapterremoval
+    path adapterlist from ch_adapterlist.collect().dump(tag: "Adapter list")
 
     output:
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("output/*{combined.fq,.se.truncated,pair1.truncated}.gz") into ch_output_from_adapterremoval_r1
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("output/*pair2.truncated.gz") optional true into ch_output_from_adapterremoval_r2
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("output/*.settings") into ch_adapterremoval_logs
-
+    
     when: 
     !params.skip_adapterremoval
 
     script:
-    base = "${r1.baseName}_L${lane}"
+    def base = "${r1.baseName}_L${lane}"
+    def adapters_to_remove = !params.clip_adapters_list ? "--adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor}" : "--adapter-list ${adapterlist}"
     //This checks whether we skip trimming and defines a variable respectively
     def preserve5p = params.preserve5p ? '--preserve5p' : '' // applies to any AR command - doesn't affect output file combination
 
     if ( seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim  && !params.mergedonly && !params.preserve5p ) {
     """
     mkdir -p output
 
-    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
 
     cat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
     
@@ -797,7 +813,7 @@ process adapter_removal {
     """
     mkdir -p output
 
-    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
 
     cat *.collapsed.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
 
@@ -810,7 +826,7 @@ process adapter_removal {
     } else if ( seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim && params.mergedonly && !params.preserve5p ) {
     """
     mkdir -p output
-    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe  --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe  --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
     
     cat *.collapsed.gz *.collapsed.truncated.gz > output/${base}.pe.combined.tmp.fq.gz
         
@@ -823,7 +839,7 @@ process adapter_removal {
     } else if ( seqtype == 'PE'  && !params.skip_collapse && !params.skip_trim && params.mergedonly && params.preserve5p ) {
     """
     mkdir -p output
-    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe  --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe  --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} --collapse ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
     
     cat *.collapsed.gz > output/${base}.pe.combined.tmp.fq.gz
     
@@ -864,15 +880,15 @@ process adapter_removal {
     } else if ( seqtype == 'PE'  && params.skip_collapse && !params.skip_trim ) {
     """
     mkdir -p output
-    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} ${preserve5p} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    AdapterRemoval --file1 ${r1} --file2 ${r2} --basename ${base}.pe --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
     
     mv ${base}.pe.pair*.truncated.gz *.settings output/
     """
     } else if ( seqtype != 'PE' && !params.skip_trim ) {
     //SE, collapse not possible, trim reads only
     """
     mkdir -p output
-    AdapterRemoval --file1 ${r1} --basename ${base}.se --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} ${preserve5p} --trimns --trimqualities --adapter1 ${params.clip_forward_adaptor} --adapter2 ${params.clip_reverse_adaptor} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
+    AdapterRemoval --file1 ${r1} --basename ${base}.se --gzip --threads ${task.cpus} --qualitymax ${params.qualitymax} ${preserve5p} --trimns --trimqualities ${adapters_to_remove} --minlength ${params.clip_readlength} --minquality ${params.clip_min_read_quality} --minadapteroverlap ${params.min_adap_overlap}
     mv *.settings *.se.truncated.gz output/
     """
     } else if ( seqtype != 'PE' && params.skip_trim ) {

nextflow.config

@@ -66,6 +66,7 @@ params {
   //Read clipping and merging parameters
   clip_forward_adaptor = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
   clip_reverse_adaptor = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
+  clip_adapters_list = null 
   clip_readlength = 30
   clip_min_read_quality = 20
   min_adap_overlap = 1

nextflow_schema.json

@@ -464,6 +464,12 @@
                     "fa_icon": "fas fa-cut",
                     "help_text": "Defines the adapter sequence to be used for the reverse read in paired end sequencing projects. This is set to `'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'` by default.\n\n> Modifies AdapterRemoval parameter: `--adapter2`"
                 },
+                "clip_adapters_list": {
+                    "type": "string",
+                    "description": "Path to AdapterRemoval adapter list file. Overrides `--clip_*_adaptor` parameters",
+                    "fa_icon": "fas fa-cut",
+                    "help_text": "Allows to supply a file with a list of adapter (combinations) to remove from all files. **Overrides** the `--clip_*_adaptor` parameters . First column represents forward strand, second column for reverse strand. You must supply all possibly combinations, one per line, and this list is applied to all files. See [AdapterRemoval documentation](https://adapterremoval.readthedocs.io/en/latest/manpage.html) for more information.\n\n> Modifies AdapterRemoval parameter: `--adapter-list`"
+                },
                 "clip_readlength": {
                     "type": "integer",
                     "default": 30,