first batch of answers (the simplest to answer) to the review

.nf-core.yml

@@ -14,5 +14,5 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 1.0dev
+  version: 1.0.0
 update: null

conf/modules.config

@@ -22,8 +22,6 @@ process {
 
     withName: 'FASTQC' {
         ext.args = '--quiet'
-        memory = '12.GB'
-
         publishDir = [
             path: { "${params.outdir}/pickup/QC" },
             mode: params.publish_dir_mode,
@@ -33,7 +31,6 @@ process {
 
     withName: 'TRIMMOMATIC' {
         ext.args2 = 'MINLEN:20'
-        memory = '12.GB'
     }
 
     withName: 'RENAMER' {

docs/usage.md

@@ -8,7 +8,7 @@
 
 ## Samplesheet input
 
-You will need to create a samplesheet that will be provided in input to `fastqrepair` as a `--input` parameter:
+You will need to create a samplesheet that will be provided to `fastqrepair` as a `--input` parameter:
 
 ```bash
 --input '[path to samplesheet file]'
@@ -19,7 +19,7 @@ The samplesheet will contain information about the samples you would like to ana
 ### Multiple runs of the same sample
 
 > [!WARNING]
-> All `sample` identifiers in a samplesheet must be unique. Rows with different `sample` identifiers but same file names are not allowed either.
+> All `sample` identifiers in a samplesheet must be unique. It is not possible to have different `sample` identifiers that refer to the same file name.
 
 Below is an example of a samplesheet containing one paired-end sample:
 
@@ -54,7 +54,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/fastqrepair --input samplesheet.csv --outdir ./results -profile docker
+nextflow run nf-core/fastqrepair --input samplesheet.csv --outdir results -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -126,11 +126,7 @@ These options are part of Nextflow and use a _single_ hyphen (pipeline parameter
 
 Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
 
-<!-- Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -->
-
-<!-- :::info
-We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
-::: -->
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
 :::info
 We highly recommend the use of Docker container for full pipeline reproducibility.

modules/local/bbmaprepair/main.nf

@@ -22,7 +22,11 @@ process BBMAPREPAIR {
     def outfastq1 = infastq1.baseName
     def outfastq2 = infastq2.baseName
     """
-    repair.sh qin=${params.qin} in=${infastq1} in2=${infastq2} out=${outfastq1}_interleaving.fastq.gz out2=${outfastq2}_interleaving.fastq.gz outsingle=${fastq[0].baseName}_singletons.fastq.gz 2> ${fastq[0].baseName}_repair.log
+    repair.sh qin=${params.qin} \
+        in=${infastq1} in2=${infastq2} \
+        out=${outfastq1}_interleaving.fastq.gz out2=${outfastq2}_interleaving.fastq.gz \
+        outsingle=${outfastq1}_singletons.fastq.gz \
+        2> ${outfastq1}_repair.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,7 +42,7 @@ process BBMAPREPAIR {
     """
     touch ${outfastq1}_interleaving.fastq.gz
     touch ${outfastq2}_interleaving.fastq.gz
-    touch ${fastq[0].baseName}_singletons.fastq.gz
+    touch ${outfastq1}_singletons.fastq.gz
     touch ${fastq[0].baseName}_repair.log
 
     cat <<-END_VERSIONS > versions.yml

modules/local/renamer/main.nf

@@ -3,13 +3,13 @@ process RENAMER {
     label 'process_single'
 
     input:
-    tuple val(meta_fastq), path(fastq)
+    tuple val(meta_fastq),  path(fastq)
     tuple val(meta_report), path(report)
 
     output:
     tuple val(meta_fastq) , path("*_repaired.fastq.gz"), emit: renamed_fastq
-    tuple val(meta_report), path("*_report.txt"), emit: renamed_report
-    path "versions.yml"                         , emit: versions
+    tuple val(meta_report), path("*_report.txt"),        emit: renamed_report
+    path "versions.yml",                                 emit: versions
 
     when:
     task.ext.when == null || task.ext.when

nextflow.config

@@ -214,7 +214,7 @@ manifest {
     name            = 'nf-core/fastqrepair'
     author          = """Tommaso Mazza"""
     homePage        = 'https://github.com/nf-core/fastqrepair'
-    description     = """A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered"""
+    description     = """A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settle reads that became disordered"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
     version         = '1.0.0'

nextflow_schema.json

@@ -2,7 +2,7 @@
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/fastqrepair/master/nextflow_schema.json",
     "title": "nf-core/fastqrepair pipeline parameters",
-    "description": "A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered",
+    "description": "A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settle reads that became disordered",
     "type": "object",
     "$defs": {
         "input_output_options": {
@@ -118,7 +118,7 @@
                     "type": "boolean",
                     "description": "Display version and exit.",
                     "fa_icon": "fas fa-question-circle",
-                    "hidden": false
+                    "hidden": true
                 },
                 "publish_dir_mode": {
                     "type": "string",