Linting for release

.github/workflows/linting.yml

@@ -22,7 +22,7 @@ jobs:
         run: npm install -g editorconfig-checker
 
       - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|cff\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
 
   Prettier:
     runs-on: ubuntu-latest

CITATION.cff

@@ -0,0 +1,34 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: sanger-tol/curationpretext v1.0.0
+message: >-
+    If you use this software, please cite it using the
+    metadata from this file.
+type: software
+authors:
+    - given-names: Damon-Lee Bernard
+      family-names: Pointon
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0003-2949-6719"
+    - given-names: Matthieu
+      family-names: Muffato
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0002-7860-3560"
+    - given-names: Ying
+      family-names: Sims
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0003-4765-4872"
+    - given-names: William
+      family-names: Eagles
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0009-0006-9956-0404"
+identifiers:
+    - type: doi
+      value: 10.5281/zenodo.XXXXXXX
+repository-code: "https://github.com/sanger-tol/curationpretext"
+license: MIT
+commit: TODO
+version: 1.0.0
+date-released: "2024-07-18"

README.md

@@ -1,15 +1,10 @@
 # ![sanger-tol/curationpretext](docs/images/curationpretext-light.png#gh-light-mode-only) ![sanger-tol/curationpretext](docs/images/curationpretext-dark.png#gh-dark-mode-only)
 
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/curationpretext/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
-
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/sanger-tol/curationpretext)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23curationpretext-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/curationpretext)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
-
 ## Introduction
 
 **sanger-tol/curationpretext** is a bioinformatics pipeline typically used in conjunction with [TreeVal](https://github.com/sanger-tol/treeval) to generate pretext maps (and optionally telomeric, gap, coverage, and repeat density plots which can be ingested into pretext) for the manual curation of high quality genomes.
@@ -127,8 +122,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use  sanger-tol/curationpretext for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:
@@ -138,7 +131,3 @@ You can cite the `nf-core` publication as follows:
 > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
 >
 > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
-
-```
-
-```

modules/local/avgcov.nf

@@ -1,6 +1,6 @@
 process AVGCOV {
     tag "${meta.id}"
-    label "process_single"
+    label 'process_single'
 
     conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/bamtobed_sort.nf

@@ -13,6 +13,9 @@ process BAMTOBED_SORT {
     tuple val(meta), path("*.bed"), emit: sorted_bed
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def prefix = args.ext.prefix ?: "${meta.id}"
     def st_cores = task.cpus > 4 ? 4 : "${task.cpus}"

modules/local/cram_filter_align_bwamem2_fixmate_sort.nf

@@ -1,6 +1,6 @@
 process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
     tag "$meta.id"
-    label "process_high"
+    label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :

modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf

@@ -1,6 +1,6 @@
 process CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
     tag "$meta.id"
-    label "process_high"
+    label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :

modules/local/extract_repeat.nf

@@ -8,7 +8,7 @@ process EXTRACT_REPEAT {
         'biocontainers/perl:5.26.2' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
     tuple val( meta ), path( "*.bed" )  , emit: bed

modules/local/extract_telo.nf

@@ -8,13 +8,16 @@ process EXTRACT_TELO {
     'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
     tuple val( meta ), file( "*bed" )   , emit: bed
     path("*bedgraph")                   , emit: bedgraph
     path "versions.yml"                 , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     shell:
     def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/local/find_telomere_regions.nf

@@ -4,14 +4,22 @@ process FIND_TELOMERE_REGIONS {
 
     container 'docker.io/library/gcc:7.1.0'
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "FIND_TELOMERE_REGIONS module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
     val (telomereseq)
 
     output:
     tuple val( meta ), file( "*.telomere" ) , emit: telomere
     path "versions.yml"                     , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/local/find_telomere_windows.nf

@@ -9,12 +9,15 @@ process FIND_TELOMERE_WINDOWS {
         'biocontainers/java-jdk:8.0.112--1' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
     tuple val( meta ), file( "*.windows" ) , emit: windows
     path "versions.yml"                    , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "1.0" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/local/gap_length.nf

@@ -8,12 +8,15 @@ process GAP_LENGTH {
     'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
     tuple val( meta ), file( "*bedgraph" )  , emit: bed
     path "versions.yml"                     , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     shell:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/local/generate_cram_csv.nf

@@ -1,16 +1,24 @@
 process GENERATE_CRAM_CSV {
     tag "${meta.id}"
-    label 'process_tiny'
+    label 'process_single'
 
     container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1'
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "GENERATE_CRAM_CSV module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
     tuple val(meta), path(crampath)
 
     output:
     tuple val(meta), path('*.csv'), emit: csv
     path "versions.yml",            emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """

modules/local/generate_genome_file.nf

@@ -8,12 +8,15 @@ process GENERATE_GENOME_FILE {
     'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( fai )
+    tuple val(meta), path(fai)
 
     output:
     tuple val( meta ), file( "my.genome" )      , emit: dotgenome
     path "versions.yml"                         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """

modules/local/get_largest_scaff.nf

@@ -9,11 +9,14 @@ process GET_LARGEST_SCAFF {
     'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
-    env largest_scaff   , emit: scaff_size
-    path "versions.yml" , emit: versions
+    tuple val(meta), env(largest_scaff),    emit: scaff_size
+    path "versions.yml",                    emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     shell:
     def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

modules/local/getminmaxpunches.nf

@@ -15,6 +15,9 @@ process GETMINMAXPUNCHES{
     tuple val(meta), path ( '*max.bed' )    , optional: true    , emit: max
     path "versions.yml"                     , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     shell:
     def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     $/

modules/local/longreadcoveragescalelog.nf

@@ -1,6 +1,6 @@
 process LONGREADCOVERAGESCALELOG {
     tag "${meta.id}"
-    label "process_single"
+    label 'process_single'
 
     conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/pretext_graph.nf

@@ -4,6 +4,11 @@ process PRETEXT_GRAPH {
 
     container "quay.io/sanger-tol/pretext:0.0.2-yy5-c3"
 
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "PRETEXT_GRAPH module does not support Conda. Please use Docker / Singularity instead."
+    }
+
     input:
     tuple val(meta),    path(pretext_file,      stageAs: 'pretext.pretext')
     tuple val(gap),     path(gap_file,          stageAs: 'gap.bed')

modules/local/reformat_intersect.nf

@@ -8,10 +8,14 @@ process REFORMAT_INTERSECT {
     'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
     tuple val( meta ), file( "*.bed" ), emit: bed
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     shell:
     def prefix = task.ext.prefix ?: "${meta.id}"

modules/local/rename_ids.nf

@@ -8,12 +8,15 @@ process RENAME_IDS {
     'docker.io/ubuntu:20.04' }"
 
     input:
-    tuple val( meta ), path( file )
+    tuple val(meta), path(file)
 
     output:
     tuple val( meta ), file( "*bed" )   , emit: bed
     path "versions.yml"                 , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     shell:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.