updated changelog, citations and output.md

.devcontainer/devcontainer.json

@@ -3,6 +3,7 @@
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
     "runArgs": ["--privileged"],
+
     // Configure tool-specific properties.
     "customizations": {
         // Configure properties specific to VS Code.
@@ -11,6 +12,7 @@
             "settings": {
                 "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
+
             // Add the IDs of extensions you want installed when the container is created.
             "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
         }

.github/CONTRIBUTING.md

@@ -90,7 +90,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 

CHANGELOG.md

@@ -3,20 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.0.0](https://github.com/nf-core/fastqrepair/releases/tag/1.0.0) - Catanzaro YellowRed [25/01/2025]
+## v[1.0.0](https://github.com/nf-core/fastqrepair/releases/tag/1.0.0) - Catanzaro YellowRed [25/01/2025]
 
 Initial release of nf-core/fastqrepair, created with the [nf-core](https://nf-co.re/) template.
 
-### Credits
+<!--
+Added
+Fixed
+Dependencies
+Deprecated
+-->
 
-Special thanks to the following for their contributions to the release:
-
-- [Sateesh Peri](https://github.com/sateeshperi)
-- [Louis Le Nézet](https://github.com/LouisLeNezet) - reviewer
-- [Anabella Trigila](https://github.com/atrigila) - reviewer
-- [James A. Fellows Yates](https://github.com/jfy133) - reviewer
-
-### Enhancements & fixes
+### `Fixed`
 
 - [PR #2](https://github.com/nf-core/fastqrepair/pull/2) - First release
 
@@ -35,3 +33,13 @@ Special thanks to the following for their contributions to the release:
 > **NB:** Dependency has been **added** if just the new version information is present.
 >
 > **NB:** Dependency has been **removed** if new version information isn't present.
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Sateesh Peri](https://github.com/sateeshperi)
+- [Louis Le Nézet](https://github.com/LouisLeNezet) - reviewer
+- [Anabella Trigila](https://github.com/atrigila) - reviewer
+- [James A. Fellows Yates](https://github.com/jfy133) - reviewer
+- [Charles Plessy](https://github.com/charles-plessy) - reviewer

CITATIONS.md

@@ -20,7 +20,7 @@
 
 - [Wipertools](https://github.com/mazzalab/fastqwiper)
 
-> Mazza, T. (2025). Wipertools. [![DOI](https://zenodo.org/badge/325529896.svg)](https://doi.org/10.5281/zenodo.14176147){: style="float:right"}
+> MazzaLab, Tommaso Mazza, & Jose F Oviedo. (2025). mazzalab/fastqwiper: v1.1.5 (v1.1.5). Zenodo. [https://doi.org/10.5281/zenodo.14774039](https://doi.org/10.5281/zenodo.14774039)
 
 - [BBMap](http://sourceforge.net/projects/bbmap/)
 

docs/output.md

@@ -23,8 +23,8 @@ The nf-core/fastqrepair pipeline is built using [Nextflow](https://www.nextflow.
 - `pipeline_info` contains report metrics generated during the [workflow execution](#pipeline-information)
 - `QC` contains [FastQC](#fastqc) QC analysis results and [MultiQC](#multiqc) reports
 - `repaired` contains repaired fastq files and relative quality reports
-  - `mysampleA_R1.fastq.gz` and `mysampleA_R2.fastq.gz` are the repaired fastq files
-  - `mysampleA_R1.report` and `mysampleA_R2.report` are the summaries of the cleaning task
+  - `mysampleA_R1.fastq.gz` (and `mysampleA_R2.fastq.gz`) are the repaired fastq files
+  - `mysampleA_R1.report` (and `mysampleA_R2.report`) are the summaries of the cleaning task
 
 </details>
 

subworkflows/local/fastq_repair_wipertools/main.nf

@@ -9,6 +9,8 @@ workflow FASTQ_REPAIR_WIPERTOOLS {
     ch_fastq // channel: [ val(meta), [ .fastq ] ]
 
     main:
+    ch_versions = Channel.empty()
+
     // decouple fastq files [sample_id = id; id is the file name]
     ch_decoupled = ch_fastq.flatMap {
         meta, fastqList -> fastqList instanceof List
@@ -21,6 +23,7 @@ workflow FASTQ_REPAIR_WIPERTOOLS {
         ch_decoupled,
         params.num_splits
     )
+    ch_versions = ch_versions.mix(WIPERTOOLS_FASTQSCATTER.out.versions.first())
 
     /* decouple chunks
     id          = the chunk file name
@@ -37,6 +40,7 @@ workflow FASTQ_REPAIR_WIPERTOOLS {
     WIPERTOOLS_FASTQWIPER {
         ch_scattered_fastq
     }
+    ch_versions = ch_versions.mix(WIPERTOOLS_FASTQWIPER.out.versions.first())
 
     // group wiped chunks
     ch_cleaned_fastq = Channel.empty()
@@ -50,6 +54,7 @@ workflow FASTQ_REPAIR_WIPERTOOLS {
     WIPERTOOLS_FASTQGATHER(
         ch_cleaned_fastq
     )
+    ch_versions = ch_versions.mix(WIPERTOOLS_FASTQGATHER.out.versions.first())
 
     // group wiping reports
     ch_gathered_report = Channel.empty()
@@ -64,18 +69,12 @@ workflow FASTQ_REPAIR_WIPERTOOLS {
     WIPERTOOLS_REPORTGATHER(
         ch_gathered_report
     )
+    ch_versions = ch_versions.mix(WIPERTOOLS_REPORTGATHER.out.versions.first())
+
     WIPERTOOLS_REPORTGATHER.out.gathered_report
     | map { meta, report -> [['id':meta.sample_id, 'single_end':meta.single_end], report]}
     | set { ch_final_reports }
 
-    // gather versions
-    ch_versions = Channel.empty()
-    ch_versions = ch_versions.mix(
-        WIPERTOOLS_FASTQSCATTER.out.versions.first(),
-        WIPERTOOLS_FASTQWIPER.out.versions.first(),
-        WIPERTOOLS_FASTQGATHER.out.versions.first(),
-        WIPERTOOLS_REPORTGATHER.out.versions.first()
-    )
 
     emit:
     wiped_fastq = WIPERTOOLS_FASTQGATHER.out.gathered_fastq  // channel: [ val(meta), [ .fastq|.fastq.gz ] ]

workflows/fastqrepair.nf

@@ -41,6 +41,7 @@ workflow FASTQREPAIR {
     // Recover corrupted gz files
     //
     GZRT (ch_fastq_ext.gz_files)
+    ch_versions = ch_versions.mix(GZRT.out.versions.first())
 
     // Join recovered gz files with non-gz files and filter empty files out
     ch_tobewiped_fastq = Channel.empty()
@@ -54,8 +55,7 @@ workflow FASTQREPAIR {
     // If all input files are empty, then skip the rest of the pipeline
     ch_tobewiped_fastq
     | ifEmpty {
-        error "No non-empty FASTQ files found after GZRT. Skipping the rest of the pipeline."
-        // log.warn "No non-empty FASTQ files found. Skipping the rest of the pipeline."
+        log.warn "No non-empty FASTQ files found after GZRT. Skipping the rest of the pipeline for ${meta.id}"
     }
 
     // If ch_tobewiped_fastq has a size < ch_samplesheet but > zero, then some files were empty and we need to log.warn them
@@ -69,13 +69,14 @@ workflow FASTQREPAIR {
         .set { subset_ids }
 
     all_ids.minus(subset_ids).subscribe{ id_list -> if (id_list.size > 0) log.warn "FASTQ files with the following meta.ids are empty: ${id_list.join(', ')}" }
-    //
 
     //
     // Make fastq compliant and wipe bad characters
     //
     ch_repaired_fastq = Channel.empty()
     FASTQ_REPAIR_WIPERTOOLS (ch_tobewiped_fastq)
+    ch_versions = ch_versions.mix(FASTQ_REPAIR_WIPERTOOLS.out.versions.first())
+
     FASTQ_REPAIR_WIPERTOOLS.out.wiped_fastq
     | map { meta, fq -> [meta.subMap('sample_id', 'single_end'), fq]}
     | map { meta, fq -> [['id':meta.sample_id, 'single_end':meta.single_end], fq]}
@@ -89,14 +90,13 @@ workflow FASTQREPAIR {
     ch_repaired_fastq.paired_end
     | groupTuple
     | set { ch_repaired_fastq_paired_end }
-    //
 
-    //
     // Settle reads pairing (re-pair, optional)
     //
     if (!params.skip_bbmap_repair) {
         // Re-pair reads
         BBMAP_REPAIR (ch_repaired_fastq_paired_end, false)
+        ch_versions = ch_versions.mix(BBMAP_REPAIR.out.versions.first())
 
         ch_repaired_fastq_paired_end_singleton = Channel.empty()
         BBMAP_REPAIR.out.repaired
@@ -106,7 +106,6 @@ workflow FASTQREPAIR {
         | set { ch_repaired_fastq_paired_end_singleton }
 
         ch_final = ch_repaired_fastq_paired_end_singleton.concat(ch_repaired_fastq.single_end)
-        ch_versions = ch_versions.mix(BBMAP_REPAIR.out.versions.first())
     } else {
         ch_final = ch_repaired_fastq_paired_end.concat(ch_repaired_fastq.single_end)
     }
@@ -115,15 +114,8 @@ workflow FASTQREPAIR {
     // Assess QC of all fastq files (both single and paired end)
     //
     FASTQC ( ch_final )
+    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
-    //
-    // Collate and save software versions
-    //
-    ch_versions = ch_versions.mix(
-        GZRT.out.versions.first(),
-        FASTQ_REPAIR_WIPERTOOLS.out.versions,
-        FASTQC.out.versions.first()
-    )
 
     softwareVersionsToYAML(ch_versions)
         .collectFile(