Merge pull request #207 from luslab/dev

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nf-core · Aug 29, 2023 · d439825 · d439825
2 parents 62a25c6 + dbea235
commit d439825
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Showing 9 changed files with 43 additions and 17 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#189](https://github.com/nf-core/cutandrun/pull/189)] - Added the name of the peak caller in the consensus peaks to make it clearer which peaks were used in the downstream reporting steps.
 - [[#196](https://github.com/nf-core/cutandrun/pull/196)] - Extended documentation for most common alternative spike-in genomes, i.e. yeast and fruit fly. Credit to smoe for this.
 - The Preseq module `lcextrap` was moved from `local` to `nf-core`
+- Updated all nf-core modules to latest versions.
 
 ### Fixes
 
@@ -29,6 +30,8 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| `bedtools` | 1.13        | 1.14        |
+| `multiqc`  | 2.30.0      | 2.31.0      |
 | `samtools` | 1.16.1      | 1.17        |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present.

diff --git a/modules.json b/modules.json
@@ -112,12 +112,12 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules", "bam_stats_samtools"]
+                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
+                        "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
                         "installed_by": ["modules", "bam_stats_samtools"]
                     },
                     "samtools/index": {
@@ -162,7 +162,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/custom_dumpsoftwareversions.nf b/modules/local/custom_dumpsoftwareversions.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path versions

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_single'
 
-    conda "bioconda::multiqc=1.14"
+    conda "bioconda::multiqc=1.15"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.15--pyhdfd78af_0' }"
 
     input:
     path multiqc_config

diff --git a/modules/local/peak_counts.nf b/modules/local/peak_counts.nf
@@ -2,10 +2,10 @@ process PEAK_COUNTS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::bedtools=2.30.0"
+    conda "bioconda::bedtools=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-        'biocontainers/bedtools:2.30.0--hc088bd4_0' }"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.31.0--hf5e1c6e_2' :
+        'biocontainers/bedtools:2.31.0--hf5e1c6e_2' }"
 
     input:
     tuple val(meta), path(bed)

diff --git a/modules/local/peak_frip.nf b/modules/local/peak_frip.nf
@@ -2,10 +2,10 @@ process PEAK_FRIP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bedtools=2.30.0"
+    conda "bioconda::bedtools=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
-        'biocontainers/bedtools:2.30.0--hc088bd4_0' }"
+        'https://depot.galaxyproject.org/singularity/bedtools:2.31.0--hf5e1c6e_2' :
+        'biocontainers/bedtools:2.31.0--hf5e1c6e_2' }"
 
     input:
     tuple val(meta), path(peaks_bed), path(fragments_bed), path(flagstat)

diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf