Merge pull request #19 from jannikseidelQBiC/updateModules

Update modules
nf-core · Mar 6, 2024 · ccc19ec · ccc19ec
2 parents 46badb4 + cb8a21a
commit ccc19ec
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Showing 7 changed files with 315 additions and 95 deletions.
diff --git a/modules.json b/modules.json
@@ -12,12 +12,12 @@
                     },
                     "blast/makeblastdb": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "a01c66c96e0bc610ad126e7adc4a94cd4acd1b48",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "d086322563bdbb08c94bf15a7db58a39ccdb1520",
+                        "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {

diff --git a/modules/local/filter.nf b/modules/local/filter.nf
@@ -2,10 +2,10 @@ process FILTER {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::seqkit=2.6.0"
+    conda "bioconda::seqkit=2.7.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit%3A2.6.0--h9ee0642_0':
-        'biocontainers/seqkit:2.6.0--h9ee0642_0'}"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.7.0--h9ee0642_0':
+        'biocontainers/seqkit:2.7.0--h9ee0642_0'}"
 
     input:
     tuple val(meta), path(fastq), path(ids_to_remove)

diff --git a/modules/local/prepare_fasta4blastn.nf b/modules/local/prepare_fasta4blastn.nf
@@ -2,10 +2,10 @@ process PREPARE_FASTA4BLASTN {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::seqkit=2.6.0"
+    conda "bioconda::seqkit=2.7.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit%3A2.6.0--h9ee0642_0':
-        'biocontainers/seqkit:2.6.0--h9ee0642_0'}"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.7.0--h9ee0642_0':
+        'biocontainers/seqkit:2.7.0--h9ee0642_0'}"
 
     input:
     tuple val(meta), path(trimmedreads), path(kraken2results)

diff --git a/modules/nf-core/blast/makeblastdb/environment.yml b/modules/nf-core/blast/makeblastdb/environment.yml
diff --git a/modules/nf-core/blast/makeblastdb/main.nf b/modules/nf-core/blast/makeblastdb/main.nf
diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test