nf-core
diff --git a/‎setup-nextflow‎
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diff --git a/‎subworkflows/nf-core/fastq_removeadapters_merge/main.nf‎
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diff --git a/‎subworkflows/nf-core/fastq_removeadapters_merge/meta.yml‎
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+// both SE and PE
+include { TRIMMOMATIC                         } from '../../../modules/nf-core/trimmomatic/main'
+include { CUTADAPT                            } from '../../../modules/nf-core/cutadapt/main'
+include { TRIMGALORE                          } from '../../../modules/nf-core/trimgalore/main'
+include { BBMAP_BBDUK                         } from '../../../modules/nf-core/bbmap/bbduk/main'
+include { LEEHOM                              } from '../../../modules/nf-core/leehom/main'
+// both SE and PE, plus merging
+include { FASTP                               } from '../../../modules/nf-core/fastp/main'
+include { ADAPTERREMOVAL as ADAPTERREMOVAL_SE } from '../../../modules/nf-core/adapterremoval/main'
+include { ADAPTERREMOVAL as ADAPTERREMOVAL_PE } from '../../../modules/nf-core/adapterremoval/main'
+// helper module for concatenating adapterremoval paired-end processed reads
+include { CAT_FASTQ                           } from '../../../modules/nf-core/cat/fastq/main'
+
+workflow FASTQ_REMOVEADAPTERS_MERGE {
+
+    take:
+    ch_input_reads                 // channel: [mandatory] meta, reads
+    val_adapter_tool               // string:  [mandatory] tool_name // choose from: ["trimmomatic", "cutadapt", "trimgalore", "bbduk", "leehom", "fastp", "adapterremoval"]
+    ch_custom_adapters_file        // channel: [optional]  {fasta,txt} // fasta, for bbduk or fastp, or txt, for adapterremoval
+    val_save_merged                // boolean: [mandatory] if true, will return the merged reads instead, for fastp and adapterremoval
+    val_fastp_discard_trimmed_pass // boolean: [mandatory] // only for fastp
+    val_fastp_save_trimmed_fail    // boolean: [mandatory] // only for fastp
+
+    main:
+
+    ch_discarded_reads    = channel.empty() // from trimmomatic, trimgalore, leehom, fastp, adapterremoval
+    ch_log                = channel.empty() // from trimmomatic, trimgalore, fastp
+    ch_report             = channel.empty() // from trimmomatic, trimgalore, fastp
+    ch_versions           = channel.empty()
+    ch_multiqc_files      = channel.empty() // from trimmomatic, cutadapt, bbduk, leehom, fastp, adapterremoval
+
+    if (val_adapter_tool == "trimmomatic") {
+        TRIMMOMATIC( ch_input_reads )
+
+        ch_processed_reads = TRIMMOMATIC.out.trimmed_reads
+        ch_discarded_reads = ch_discarded_reads.mix(TRIMMOMATIC.out.unpaired_reads.transpose()) // .transpose() because paired reads will output 2 unpaired files in an array
+        ch_log             = TRIMMOMATIC.out.trim_log
+        ch_report          = TRIMMOMATIC.out.summary
+        ch_versions        = ch_versions.mix(TRIMMOMATIC.out.versions.first())
+        ch_multiqc_files   = ch_multiqc_files.mix(TRIMMOMATIC.out.out_log)
+    } else if (val_adapter_tool == "cutadapt") {
+        CUTADAPT( ch_input_reads )
+
+        ch_processed_reads = CUTADAPT.out.reads
+        ch_multiqc_files   = ch_multiqc_files.mix(CUTADAPT.out.log)
+    } else if (val_adapter_tool == "trimgalore") {
+        TRIMGALORE( ch_input_reads )
+
+        ch_processed_reads = TRIMGALORE.out.reads
+        ch_discarded_reads = ch_discarded_reads.mix(TRIMGALORE.out.unpaired)
+        ch_log             = TRIMGALORE.out.log
+        ch_report          = TRIMGALORE.out.html.mix(TRIMGALORE.out.zip)
+    } else if (val_adapter_tool == "bbduk") {
+        BBMAP_BBDUK( ch_input_reads, ch_custom_adapters_file )
+
+        ch_processed_reads = BBMAP_BBDUK.out.reads
+        ch_versions        = ch_versions.mix(BBMAP_BBDUK.out.versions.first())
+        ch_multiqc_files   = ch_multiqc_files.mix(BBMAP_BBDUK.out.log)
+    } else if (val_adapter_tool == "leehom") {
+        LEEHOM( ch_input_reads )
+
+        ch_processed_reads = LEEHOM.out.fq_pass
+            .join(LEEHOM.out.unmerged_r1_fq_pass, by: 0, remainder: true)
+            .join(LEEHOM.out.unmerged_r2_fq_pass, by: 0, remainder: true)
+            .map { meta, single, r1, r2 ->
+                if (meta.single_end) {
+                    return [meta, single]
+                } else {
+                    return [meta, [r1, r2]]
+                }
+            }
+        ch_discarded_reads = ch_discarded_reads.mix(LEEHOM.out.fq_fail, LEEHOM.out.unmerged_r1_fq_fail, LEEHOM.out.unmerged_r2_fq_fail)
+        ch_versions        = ch_versions.mix(LEEHOM.out.versions.first())
+        ch_multiqc_files   = ch_multiqc_files.mix(LEEHOM.out.log)
+    } else if (val_adapter_tool == "fastp") {
+        FASTP(
+            ch_input_reads.map { meta, files ->  [ meta, files, ch_custom_adapters_file ] },
+            val_fastp_discard_trimmed_pass,
+            val_fastp_save_trimmed_fail,
+            val_save_merged
+        )
+
+        if (val_save_merged) {
+            ch_processed_reads = FASTP.out.reads_merged
+        } else {
+            ch_processed_reads = FASTP.out.reads
+        }
+        ch_discarded_reads = ch_discarded_reads.mix(FASTP.out.reads_fail.transpose()) // .transpose() because paired reads have 3 fail files in an array
+        ch_log             = FASTP.out.log
+        ch_report          = FASTP.out.html
+        ch_versions        = ch_versions.mix(FASTP.out.versions.first())
+        ch_multiqc_files   = ch_multiqc_files.mix(FASTP.out.json)
+    } else if (val_adapter_tool == "adapterremoval") {
+        ch_adapterremoval_in = ch_input_reads
+            .branch { meta, _reads ->
+                single: meta.single_end
+                paired: !meta.single_end
+            }
+
+        ADAPTERREMOVAL_SE( ch_adapterremoval_in.single, ch_custom_adapters_file )
+        ADAPTERREMOVAL_PE( ch_adapterremoval_in.paired, ch_custom_adapters_file )
+
+        if (val_save_merged) { // merge
+            ch_concat_fastq = channel.empty()
+                .mix(
+                    ADAPTERREMOVAL_PE.out.collapsed,
+                    ADAPTERREMOVAL_PE.out.collapsed_truncated,
+                    ADAPTERREMOVAL_PE.out.singles_truncated,
+                )
+                .map { meta, reads ->
+                    def meta_new = meta.clone()
+                    meta_new.single_end = true
+                    [meta_new, reads]
+                }
+                .groupTuple()
+                // Paired-end reads cause a nested tuple during grouping.
+                // We want to present a flat list of files to `CAT_FASTQ`.
+                .map { meta, fastq -> [meta, fastq.flatten()] }
+
+            CAT_FASTQ( ch_concat_fastq )
+
+            ch_processed_reads = CAT_FASTQ.out.reads.mix(ADAPTERREMOVAL_SE.out.singles_truncated)
+        } else { // no merge
+            ch_processed_reads = ADAPTERREMOVAL_PE.out.paired_truncated.mix(ADAPTERREMOVAL_SE.out.singles_truncated)
+        }
+        ch_discarded_reads    = ch_discarded_reads.mix(ADAPTERREMOVAL_SE.out.discarded, ADAPTERREMOVAL_PE.out.discarded)
+        ch_versions           = ch_versions.mix(ADAPTERREMOVAL_SE.out.versions.first(), ADAPTERREMOVAL_PE.out.versions.first())
+        ch_multiqc_files      = ch_multiqc_files.mix(ADAPTERREMOVAL_PE.out.settings, ADAPTERREMOVAL_SE.out.settings)
+    } else {
+        error('Please choose one of the available adapter removal and merging tools: ["trimmomatic", "cutadapt", "trimgalore", "bbduk", "leehom", "fastp", "adapterremoval"]')
+    }
+
+    emit:
+    processed_reads    = ch_processed_reads    // channel: [ val(meta), [ fastq.gz ] ]
+    discarded_reads    = ch_discarded_reads    // channel: [ val(meta), [ fastq.gz ] ]
+    logfile            = ch_log                // channel: [ val(meta), [ {log,txt} ] ]
+    report             = ch_report             // channel: [ val(meta), [ {summary,html,zip} ] ]
+    versions           = ch_versions           // channel: [ versions.yml ]
+    multiqc_files      = ch_multiqc_files
+}
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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "fastq_removeadapters_merge"
+description: Remove adapters and merge reads based on various module choices
+keywords:
+  - adapters
+  - removal
+  - short reads
+  - merge
+  - trim
+components:
+  - trimmomatic
+  - cutadapt
+  - trimgalore
+  - bbmap/bbduk
+  - leehom
+  - fastp
+  - adapterremoval
+  - cat/fastq
+input:
+  - ch_input_reads:
+      type: file
+      description: |
+        List of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
+        Structure: [ val(meta), [ path(reads) ] ]
+  - val_adapter_tool:
+      type: string
+      description: |
+        Choose one of the available adapter removal and/or merging tools
+      enum: ["trimmomatic", "cutadapt", "trimgalore", "bbduk", "leehom", "fastp", "adapterremoval"]
+  - ch_custom_adapters_file:
+      type: file
+      description: |
+        Optional reference files, containing adapter and/or contaminant sequences for removal.
+        In fasta format for bbmap/bbduk and fastp, or in text format for AdapterRemoval (one adapter per line).
+  - val_save_merged:
+      type: boolean
+      description: |
+        Specify true to output merged reads instead
+        Used by fastp and adapterremoval
+  - val_fastp_discard_trimmed_pass:
+      type: boolean
+      description: |
+        Used only by fastp.
+        Specify true to not write any reads that pass trimming thresholds from the fastp process.
+        This can be used to use fastp for the output report only.
+  - val_fastp_save_trimmed_fail:
+      type: boolean
+      description: |
+        Used only by fastp.
+        Specify true to save files that failed to pass fastp trimming thresholds
+output:
+  - processed_reads:
+      type: file
+      description: |
+        Structure: [ val(meta), path(fastq.gz) ]
+        The trimmed/modified single or paired end or merged fastq reads
+      pattern: "*.fastq.gz"
+  - discarded_reads:
+      type: file
+      description: |
+        Structure: [ val(meta), path(fastq.gz) ]
+        The discarded reads
+      pattern: "*.fastq.gz"
+  - logfile:
+      type: file
+      description: |
+        Execution log file
+        (trimmomatic {log}, trimgalore {txt}, fastp {log})
+      pattern: "*.{log,txt}"
+  - report:
+      type: file
+      description: |
+        Execution report
+        (trimmomatic {summary}, trimgalore {html,zip}, fastp {html})
+      pattern: "*.{summary,html,zip}"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+  - multiqc_files:
+      type: file
+      description: |
+        MultiQC-compatible output files from tools used in preprocessing
+        (trimmomatic, cutadapt, bbduk, leehom, fastp, adapterremoval)
+authors:
+  - "@kornkv"
+  - "@vagkaratzas"
+maintainers:
+  - "@kornkv"
+  - "@vagkaratzas"