got PIRATE working and changed some docker repos so they work

nf-core · Jul 17, 2023 · 4ba75a7 · 4ba75a7
1 parent 4f44a00
commit 4ba75a7
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Showing 7 changed files with 14 additions and 6 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -86,4 +86,8 @@ process {
     withName: FILTER_ASSEMBLY {
         ext.args = '--cov_cutoff 1 --len_cutoff 100'
     }
+
+    withName: BAKTA_BAKTA {
+        ext.args = '--force'
+    }
 }
diff --git a/modules/local/bgzip_make_gzip.nf b/modules/local/bgzip_make_gzip.nf
@@ -5,7 +5,7 @@ process BGZIP_MAKE_GZIP {
     conda "bioconda::tabix=1.11"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
-        'biocontainers/tabix:1.11--hdfd78af_0' }"
+        'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input)

diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf
diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf
diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf