[MODIF] remove enable_conda optoin

.github/workflows/awsfulltest.yml

@@ -15,9 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## v1.4.0dev
+## v1.4.0 - 2023-04-01
 
 ### `Added`
 

assets/methods_description_template.yml

@@ -3,7 +3,7 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/hic Methods Description"
 section_href: "https://github.com/nf-core/hic"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
@@ -12,6 +12,7 @@ data: |
   <pre><code>${workflow.commandLine}</code></pre>
   <h4>References</h4>
   <ul>
+    <li>Servant, N., Ewels, P. A., Peltzer, A., Garcia, M. U. (2021) nf-core/hic. Zenodo. https://doi.org/10.5281/zenodo.2669512</li>
     <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
     <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
   </ul>

modules/local/cooltools/eigscis.nf

@@ -6,7 +6,7 @@ process COOLTOOLS_EIGSCIS {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377" : null)
+    conda "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' :
         'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"

modules/local/cooltools/insulation.nf

@@ -6,7 +6,7 @@ process COOLTOOLS_INSULATION {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::cooltools=0.5.1" : null)
+    conda "bioconda::cooltools=0.5.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' :
         'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }"

modules/local/hicexplorer/hicFindTADs.nf

@@ -5,7 +5,7 @@
 process HIC_FIND_TADS {
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
+    conda "bioconda::hicexplorer=3.7.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
         'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"

modules/local/hicexplorer/hicPlotDistVsCounts.nf

@@ -6,7 +6,7 @@ process HIC_PLOT_DIST_VS_COUNTS {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
+    conda "bioconda::hicexplorer=3.7.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
         'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"

modules/local/hicpro/bowtie2_merge.nf

@@ -2,7 +2,7 @@ process MERGE_BOWTIE2{
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
         'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

modules/local/hicpro/build_contact_maps.nf

@@ -2,7 +2,7 @@ process BUILD_CONTACT_MAPS{
   tag "${meta.id}"
   label 'process_high_memory'
 
-  conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+  conda "conda-forge::sed=4.7"
   container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
       'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
       'ubuntu:20.04' }"

modules/local/hicpro/combine_mates.nf

@@ -2,7 +2,7 @@ process COMBINE_MATES {
     tag "${meta.id}"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0" : null)
+    conda "conda-forge::python=3.9  bioconda::pysam=0.19.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
         'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"

modules/local/hicpro/dnase_mapping_stats.nf

@@ -2,7 +2,7 @@ process MAPPING_STATS_DNASE {
     tag "$sample = $bam"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    conda "bioconda::samtools=1.15.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
         'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

modules/local/hicpro/get_restriction_fragments.nf

@@ -2,7 +2,7 @@ process GET_RESTRICTION_FRAGMENTS {
     tag "$res_site"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9 conda-forge::numpy=1.22.3" : null)
+    conda "conda-forge::python=3.9 conda-forge::numpy=1.22.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
         'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"

modules/local/hicpro/get_valid_interaction.nf

@@ -2,7 +2,7 @@ process GET_VALID_INTERACTION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" : null)
+    conda "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
         'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"

modules/local/hicpro/get_valid_interaction_dnase.nf

@@ -2,7 +2,7 @@ process GET_VALID_INTERACTION_DNASE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13" : null)
+    conda "conda-forge::python=3.9  bioconda::pysam=0.19.0 bioconda::bx-python=0.8.13"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
         'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"

modules/local/hicpro/hicpro2pairs.nf

@@ -2,7 +2,7 @@ process HICPRO2PAIRS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null)
+    conda "bioconda::pairix=0.3.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
         'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"

modules/local/hicpro/merge_stats.nf

@@ -2,7 +2,7 @@ process MERGE_STATS {
     tag "${meta.id}"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9" : null)
+    conda "conda-forge::python=3.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
         'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"

modules/local/hicpro/merge_valid_interaction.nf

@@ -2,7 +2,7 @@ process MERGE_VALID_INTERACTION {
     tag "$prefix"
     label 'process_high_memory'
 
-    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+    conda "conda-forge::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'ubuntu:20.04' }"

modules/local/hicpro/run_ice.nf

@@ -2,7 +2,7 @@ process ICE_NORMALIZATION{
     tag "${meta.id}"
     label 'process_high_memory'
 
-    conda (params.enable_conda ? "conda-forge::python=3.9  bioconda::iced=0.5.10 conda-forge::numpy=1.22.3" : null)
+    conda "conda-forge::python=3.9 bioconda::iced=0.5.10 conda-forge::numpy=1.22.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0' :
         'quay.io/biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0'}"

modules/local/hicpro/trim_reads.nf

@@ -2,7 +2,7 @@ process TRIM_READS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'ubuntu:20.04' }"

modules/local/multiqc.nf

 process MULTIQC {
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+    conda "bioconda::multiqc=1.13"
      container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
         'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"