Addd FASTP adadapter list

conf/modules.config

@@ -62,7 +62,7 @@ process {
         ext.args   = [
             // trimming options
             params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
-            params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
+            params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
             // filtering options
             "--length_required ${params.shortread_qc_minlength}",
             (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
@@ -82,8 +82,8 @@ process {
             params.shortread_qc_excludeunmerged ? '' : "--include_unmerged",
             // trimming options
             params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
-            params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
+            params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
-            params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
+            params.shortread_qc_adapterlist ? "" : params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
             // filtering options
             "--length_required ${params.shortread_qc_minlength}",
             params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''

modules.json

@@ -55,7 +55,7 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "1e49f31e93c56a3832833eef90a02d3cde5a3f7e"
                     },
                     "fastqc": {
                         "branch": "master",

modules/nf-core/fastp/main.nf

@@ -9,6 +9,7 @@ process FASTP {
 
     input:
     tuple val(meta), path(reads)
+    path  adapter_fasta
     val   save_trimmed_fail
     val   save_merged
 
@@ -27,6 +28,7 @@ process FASTP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def adapter_list = adapter_fasta ? "--adapter_fasta ${adapter_fasta}" : ""
     def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
     // Added soft-links to original fastqs for consistent naming in MultiQC
     // Use single ended for interleaved. Add --interleaved_in in config.
@@ -40,6 +42,7 @@ process FASTP {
             --thread $task.cpus \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
+            $adapter_list \\
             $fail_fastq \\
             $args \\
             2> ${prefix}.fastp.log \\
@@ -61,6 +64,7 @@ process FASTP {
             --thread $task.cpus \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
+            $adapter_list \\
             $fail_fastq \\
             $args \\
             2> ${prefix}.fastp.log
@@ -82,6 +86,7 @@ process FASTP {
             --out2 ${prefix}_2.fastp.fastq.gz \\
             --json ${prefix}.fastp.json \\
             --html ${prefix}.fastp.html \\
+            $adapter_list \\
             $fail_fastq \\
             $merge_fastq \\
             --thread $task.cpus \\

modules/nf-core/fastp/meta.yml

@@ -23,6 +23,10 @@ input:
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively. If you wish to run interleaved paired-end data,  supply as single-end data
         but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.
+  - adapter_fasta:
+      type: file
+      description: File in FASTA format containing possible adapters to remove.
+      pattern: "*.{fasta,fna,fas,fa}"
   - save_trimmed_fail:
       type: boolean
       description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`

nextflow_schema.json

@@ -107,8 +107,8 @@
                 "shortread_qc_adapterlist": {
                     "type": "string",
                     "default": "None",
-                    "fa_icon": "fas fa-list-ul",
+                    "description": "Specify a list of all possible adapters to trim. Overrides --shortread_qc_adapter1/2. Formats: .txt (AdapterRemoval) or .fasta. (fastp).",
-                    "help_text": "This affects AdapterRemoval. It will replace default adapters or whatever is supplied in `--shortread_qc_adapter{1,2}`.\n\nThis allows you to mix libraries built with different adapters into one run.\n\n> Modifies tool parameter(s):\n> - AdapterRemoval: `--adapter-list`."
+                    "help_text": "Allows to supply a file with a list of adapter (combinations) to remove from all files. \n\nOverrides the --shortread_qc_adapter1/--shortread_qc_adapter2 parameters . \n\nFor AdapterRemoval this consists of a two column table with a `.txt` extension: 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 for more information.\n\nFor fastp this consists of a standard FASTA format with a `.fasta`/`.fa`/`.fna`/`.fas` extension. The adapter sequence in this file should be at least 6bp long, otherwise it will be skipped. fastp trims the adapters present in the FASTA file one by one.\n\n> Modifies AdapterRemoval parameter: --adapter-list\n> Modifies fastp parameter: --adapter_fasta"
                 },
                 "shortread_qc_mergepairs": {
                     "type": "boolean",

subworkflows/local/shortread_fastp.nf

@@ -8,6 +8,7 @@ include { FASTP as FASTP_PAIRED       } from '../../modules/nf-core/fastp/main'
 workflow SHORTREAD_FASTP {
     take:
     reads // [[meta], [reads]]
+    adapterlist
 
     main:
     ch_versions           = Channel.empty()
@@ -19,9 +20,9 @@ workflow SHORTREAD_FASTP {
                                 paired: it[0]['single_end'] == false
                             }
 
-    FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
+    FASTP_SINGLE ( ch_input_for_fastp.single, adapterlist, false, false )
     // Last parameter here turns on merging of PE data
-    FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_qc_mergepairs )
+    FASTP_PAIRED ( ch_input_for_fastp.paired, adapterlist, false, params.shortread_qc_mergepairs )
 
     if ( params.shortread_qc_mergepairs ) {
         ch_fastp_reads_prepped_pe = FASTP_PAIRED.out.reads_merged

subworkflows/local/shortread_preprocessing.nf

@@ -18,7 +18,7 @@ workflow SHORTREAD_PREPROCESSING {
     ch_multiqc_files  = Channel.empty()
 
     if ( params.shortread_qc_tool == "fastp" ) {
-        ch_processed_reads = SHORTREAD_FASTP ( reads ).reads
+        ch_processed_reads = SHORTREAD_FASTP ( reads, adapterlist ).reads
         ch_versions        =  ch_versions.mix( SHORTREAD_FASTP.out.versions )
         ch_multiqc_files   =  ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
     } else if ( params.shortread_qc_tool == "adapterremoval" ) {

workflows/taxprofiler.nf

@@ -103,7 +103,12 @@ workflow TAXPROFILER {
 
     ch_versions = Channel.empty()
     ch_multiqc_logo= Channel.fromPath("$projectDir/docs/images/nf-core-taxprofiler_logo_custom_light.png")
-    ch_adapterlist_for_shortreadqc = params.shortread_qc_adapterlist ? file(params.shortread_qc_adapterlist) : []
+    adapterlist = params.shortread_qc_adapterlist ? file(params.shortread_qc_adapterlist) : []
+
+    if ( params.shortread_qc_adapterlist ) {
+        if ( params.shortread_qc_tool == 'adapterremoval' && !(adapterlist.extension == 'txt') ) error "[nf-core/taxprofiler] ERROR: AdapterRemoval2 adapter list requires a `.txt` format and extension. Check input: --shortread_qc_adapterlist ${params.shortread_qc_adapterlist}"
+        if ( params.shortread_qc_tool == 'fastp' && !adapterlist.extension.matches(".*(fa|fasta|fna|fas)") ) error "[nf-core/taxprofiler] ERROR: fastp adapter list requires a `.fasta` format and extension (or fa, fas, fna). Check input: --shortread_qc_adapterlist ${params.shortread_qc_adapterlist}"
+    }
 
     /*
         SUBWORKFLOW: Read in samplesheet, validate and stage input files
@@ -134,10 +139,8 @@ workflow TAXPROFILER {
         SUBWORKFLOW: PERFORM PREPROCESSING
     */
 
-    ch_adapterlist_for_shortreadqc
-
     if ( params.perform_shortread_qc ) {
-        ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq, ch_adapterlist_for_shortreadqc ).reads
+        ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq, adapterlist ).reads
         ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
     } else {
         ch_shortreads_preprocessed = INPUT_CHECK.out.fastq