From 60a8656e6d96b8ab2ae2a7993ca059b4d99ed989 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Wed, 4 Jan 2023 12:47:25 +0100
Subject: [PATCH] [MODIF] remove enable_conda optoin
---
.github/workflows/awsfulltest.yml | 3 ---
CHANGELOG.md | 2 +-
assets/methods_description_template.yml | 3 ++-
modules/local/cooltools/eigscis.nf | 2 +-
modules/local/cooltools/insulation.nf | 2 +-
modules/local/hicexplorer/hicFindTADs.nf | 2 +-
modules/local/hicexplorer/hicPlotDistVsCounts.nf | 2 +-
modules/local/hicpro/bowtie2_merge.nf | 2 +-
modules/local/hicpro/build_contact_maps.nf | 2 +-
modules/local/hicpro/combine_mates.nf | 2 +-
modules/local/hicpro/dnase_mapping_stats.nf | 2 +-
modules/local/hicpro/get_restriction_fragments.nf | 2 +-
modules/local/hicpro/get_valid_interaction.nf | 2 +-
modules/local/hicpro/get_valid_interaction_dnase.nf | 2 +-
modules/local/hicpro/hicpro2pairs.nf | 2 +-
modules/local/hicpro/merge_stats.nf | 2 +-
modules/local/hicpro/merge_valid_interaction.nf | 2 +-
modules/local/hicpro/run_ice.nf | 2 +-
modules/local/hicpro/trim_reads.nf | 2 +-
modules/local/multiqc.nf | 2 +-
modules/local/split_cooler_dump.nf | 2 +-
nextflow.config | 6 ++----
nextflow_schema.json | 6 ------
23 files changed, 23 insertions(+), 33 deletions(-)
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index c528fff..ad7e2dd 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.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: ${{ secrets.TOWER_ACCESS_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b266730..50100f6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## v1.4.0dev
+## v1.4.0 - 2023-04-01
### `Added`
diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index 5b51ef5..2f0a308 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -3,7 +3,7 @@ description: "Suggested text and references to use when describing pipeline usag
section_name: "nf-core/hic Methods Description"
section_href: "https://github.com/nf-core/hic"
plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
## You inject any metadata in the Nextflow '${workflow}' object
data: |
<h4>Methods</h4>
@@ -12,6 +12,7 @@ data: |
<pre><code>${workflow.commandLine}</code></pre>
<h4>References</h4>
<ul>
+ <li>Servant, N., Ewels, P. A., Peltzer, A., Garcia, M. U. (2021) nf-core/hic. Zenodo. https://doi.org/10.5281/zenodo.2669512</li>
<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
<li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
</ul>
diff --git a/modules/local/cooltools/eigscis.nf b/modules/local/cooltools/eigscis.nf
index 29a099c..feaa300 100644
--- a/modules/local/cooltools/eigscis.nf
+++ b/modules/local/cooltools/eigscis.nf
@@ -6,7 +6,7 @@ process COOLTOOLS_EIGSCIS {
tag "${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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' :
'quay.io/biocontainers/mulled-v2-c81d8d6b6acf4714ffaae1a274527a41958443f6:cc7ea58b8cefc76bed985dcfe261cb276ed9e0cf-0' }"
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
index 6557b98..8a9127e 100644
--- a/modules/local/cooltools/insulation.nf
+++ b/modules/local/cooltools/insulation.nf
@@ -6,7 +6,7 @@ process COOLTOOLS_INSULATION {
tag "${meta.id}"
label 'process_medium'
- conda (params.enable_conda ? "bioconda::cooltools=0.5.1" : null)
+ conda "bioconda::cooltools=0.5.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cooltools:0.5.1--py37h37892f8_0' :
'quay.io/biocontainers/cooltools:0.5.1--py37h37892f8_0' }"
diff --git a/modules/local/hicexplorer/hicFindTADs.nf b/modules/local/hicexplorer/hicFindTADs.nf
index 6946e63..b6cae33 100644
--- a/modules/local/hicexplorer/hicFindTADs.nf
+++ b/modules/local/hicexplorer/hicFindTADs.nf
@@ -5,7 +5,7 @@
process HIC_FIND_TADS {
label 'process_medium'
- conda (params.enable_conda ? "bioconda::hicexplorer=3.7.2" : null)
+ conda "bioconda::hicexplorer=3.7.2"
container "${ 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' }"
diff --git a/modules/local/hicexplorer/hicPlotDistVsCounts.nf b/modules/local/hicexplorer/hicPlotDistVsCounts.nf
index 86e9e33..3e37d3f 100644
--- a/modules/local/hicexplorer/hicPlotDistVsCounts.nf
+++ b/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' }"
diff --git a/modules/local/hicpro/bowtie2_merge.nf b/modules/local/hicpro/bowtie2_merge.nf
index ed6817c..7a4e96b 100644
--- a/modules/local/hicpro/bowtie2_merge.nf
+++ b/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' }"
diff --git a/modules/local/hicpro/build_contact_maps.nf b/modules/local/hicpro/build_contact_maps.nf
index 18ed243..fd633a9 100644
--- a/modules/local/hicpro/build_contact_maps.nf
+++ b/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' }"
diff --git a/modules/local/hicpro/combine_mates.nf b/modules/local/hicpro/combine_mates.nf
index c0a8063..da95be8 100644
--- a/modules/local/hicpro/combine_mates.nf
+++ b/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'}"
diff --git a/modules/local/hicpro/dnase_mapping_stats.nf b/modules/local/hicpro/dnase_mapping_stats.nf
index 9505298..64cb079 100644
--- a/modules/local/hicpro/dnase_mapping_stats.nf
+++ b/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' }"
diff --git a/modules/local/hicpro/get_restriction_fragments.nf b/modules/local/hicpro/get_restriction_fragments.nf
index 7b6b6a4..affc2d9 100644
--- a/modules/local/hicpro/get_restriction_fragments.nf
+++ b/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'}"
diff --git a/modules/local/hicpro/get_valid_interaction.nf b/modules/local/hicpro/get_valid_interaction.nf
index 4fef34d..cc14837 100644
--- a/modules/local/hicpro/get_valid_interaction.nf
+++ b/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'}"
diff --git a/modules/local/hicpro/get_valid_interaction_dnase.nf b/modules/local/hicpro/get_valid_interaction_dnase.nf
index 08a019f..0cb5883 100644
--- a/modules/local/hicpro/get_valid_interaction_dnase.nf
+++ b/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'}"
diff --git a/modules/local/hicpro/hicpro2pairs.nf b/modules/local/hicpro/hicpro2pairs.nf
index 08222af..2ba2a90 100644
--- a/modules/local/hicpro/hicpro2pairs.nf
+++ b/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' }"
diff --git a/modules/local/hicpro/merge_stats.nf b/modules/local/hicpro/merge_stats.nf
index 757ec23..b25dc8a 100644
--- a/modules/local/hicpro/merge_stats.nf
+++ b/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'}"
diff --git a/modules/local/hicpro/merge_valid_interaction.nf b/modules/local/hicpro/merge_valid_interaction.nf
index c5b716d..29e568a 100644
--- a/modules/local/hicpro/merge_valid_interaction.nf
+++ b/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' }"
diff --git a/modules/local/hicpro/run_ice.nf b/modules/local/hicpro/run_ice.nf
index bf9bf6e..0aaa3d5 100644
--- a/modules/local/hicpro/run_ice.nf
+++ b/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'}"
diff --git a/modules/local/hicpro/trim_reads.nf b/modules/local/hicpro/trim_reads.nf
index 1585591..5a96df4 100644
--- a/modules/local/hicpro/trim_reads.nf
+++ b/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' }"
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
index 8af7656..c4bc63e 100644
--- a/modules/local/multiqc.nf
+++ b/modules/local/multiqc.nf
@@ -1,7 +1,7 @@
process MULTIQC {
label 'process_medium'
- conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
+ conda "bioconda::multiqc=1.13"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
diff --git a/modules/local/split_cooler_dump.nf b/modules/local/split_cooler_dump.nf
index fbe1428..cb44b6d 100644
--- a/modules/local/split_cooler_dump.nf
+++ b/modules/local/split_cooler_dump.nf
@@ -2,7 +2,7 @@ process SPLIT_COOLER_DUMP {
tag "$meta.id"
label 'process_low'
- conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
+ conda "conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
diff --git a/nextflow.config b/nextflow.config
index cfddfeb..83e09fb 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -111,9 +111,7 @@ params {
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,digest'
- enable_conda = false
-
-
+
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
@@ -269,7 +267,7 @@ manifest {
description = """Analysis of Chromosome Conformation Capture data (Hi-C)"""
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1'
- version = '1.4.0dev'
+ version = '1.4.0'
doi = ''
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8bce173..96e9e09 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -520,12 +520,6 @@
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
- },
- "enable_conda": {
- "type": "boolean",
- "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
- "hidden": true,
- "fa_icon": "fas fa-bacon"
}
}
}
--
GitLab