From 6dde1ade8b4fbef368ed639d847dd30537f0a991 Mon Sep 17 00:00:00 2001 From: mazzalab Date: Wed, 30 Oct 2024 15:09:44 +0100 Subject: [PATCH] first batch of answers (the simplest to answer) to the review --- .nf-core.yml | 2 +- conf/modules.config | 3 --- docs/usage.md | 12 ++++-------- modules/local/bbmaprepair/main.nf | 8 ++++++-- modules/local/renamer/main.nf | 6 +++--- nextflow.config | 2 +- nextflow_schema.json | 4 ++-- 7 files changed, 17 insertions(+), 20 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 0c4e162..154b940 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -14,5 +14,5 @@ template: outdir: . skip_features: - igenomes - version: 1.0dev + version: 1.0.0 update: null diff --git a/conf/modules.config b/conf/modules.config index da15c7d..0f19928 100644 --- a/conf/modules.config +++ b/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' { diff --git a/docs/usage.md b/docs/usage.md index 205bcd8..f35c3b8 100644 --- a/docs/usage.md +++ b/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 container for full pipeline reproducibility. diff --git a/modules/local/bbmaprepair/main.nf b/modules/local/bbmaprepair/main.nf index 6503e54..c99fe37 100644 --- a/modules/local/bbmaprepair/main.nf +++ b/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 ${fastq[0].baseName}_repair.log cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/renamer/main.nf b/modules/local/renamer/main.nf index b3e81f2..875f69c 100644 --- a/modules/local/renamer/main.nf +++ b/modules/local/renamer/main.nf @@ -3,13 +3,13 @@ process RENAMER { label 'process_single' input: - tuple val(meta_fastq), path(fastq) + tuple val(meta_fastq), path(fastq) tuple val(meta_report), path(report) output: tuple val(meta_fastq) , path("*_repaired.fastq.gz"), emit: renamed_fastq - tuple val(meta_report), path("*_report.txt"), emit: renamed_report - path "versions.yml" , emit: versions + tuple val(meta_report), path("*_report.txt"), emit: renamed_report + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when diff --git a/nextflow.config b/nextflow.config index 8d3cdcb..0af49cf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -214,7 +214,7 @@ manifest { name = 'nf-core/fastqrepair' author = """Tommaso Mazza""" homePage = 'https://github.com/nf-core/fastqrepair' - description = """A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered""" + description = """A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settle reads that became disordered""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' version = '1.0.0' diff --git a/nextflow_schema.json b/nextflow_schema.json index 5526bf9..ea9f12e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,7 +2,7 @@ "$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",