update to mulled containers

Author: mykle hoban

conf/modules.config

@@ -20,17 +20,25 @@ process {
 
     withName: RMARKDOWNNOTEBOOK {
         conda = { [
-            'conda-forge::r-rmarkdown=2.29',
-            'conda-forge::r-knitr=1.50',
-            'conda-forge::r-yaml=2.3.10',
-            'conda-forge::r-plotly=4.10.4',
-            'conda-forge::r-dt=0.33',
-            'conda-forge::r-dplyr=1.1.4',
-            'conda-forge::r-readr=2.1.5',
-            'conda-forge::r-forcats=1.0.0',
-            'conda-forge::r-paletteer=1.6.0'
+            'r-rmarkdown=2.29',
+            'r-yaml=2.3.10',
+            'r-tidyr=1.3.1',
+            'r-data.table=1.17.8',
+            'r-knitr=1.50',
+            'r-plotly=4.11.0',
+            'r-dt=0.33',
+            'r-stringr=1.5.1',
+            'r-purrr=1.1.0',
+            'r-paletteer=1.6.0',
+            'r-htmltools=0.5.8.1',
+            'r-ggplot2=3.5.2',
+            'r-forcats=1.0.0',
+            'r-scales=1.4.0',
+            'r-jsonlite=2.0.0'
         ].join(' ').trim() }
-        container = { "fishbotherer/buildreport:1.0.1" }
+        container = { "${ workflow.containerEngine == 'singularity' && !ext.singularity_pull_docker_container ?
+            'https://depot.galaxyproject.org/singularity/mulled-v2-b5ef69f92fe3bbdbe29f16d80675330b2bd45a66:a66dc1806b3ac5c904f1d0359e0504581f5495cd-0' :
+            'biocontainers/mulled-v2-b5ef69f92fe3bbdbe29f16d80675330b2bd45a66:a66dc1806b3ac5c904f1d0359e0504581f5495cd-0' }" }
         publishDir = [
             [
                 path: { "${params.outdir}/report" },

modules/local/extractsequences/environment.yml

@@ -4,6 +4,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - bioconda::bioconductor-rsamtools=2.22.0
   - conda-forge::r-optparse=1.7.5
   - conda-forge::r-data.table=1.17.8
-  - bioconda::bioconductor-rsamtools=2.22.0

modules/local/extractsequences/main.nf

@@ -3,10 +3,9 @@ process EXTRACT_SEQUENCES {
     label 'process_single_mem'
 
     conda "${moduleDir}/environment.yml"
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    //     'https://depot.galaxyproject.org/singularity/mulled-v2-61c59287265e27f2c4589cfc90013ef6c2c6acf1:fb3e48060a8c0e5108b1b60a2ad7e090cfb9eee5-0':
-    //     'biocontainers/mulled-v2-61c59287265e27f2c4589cfc90013ef6c2c6acf1:fb3e48060a8c0e5108b1b60a2ad7e090cfb9eee5-0' }"
-    container 'fishbotherer/extractr:1.0.0'
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-24c2519e6f79268102473627bccca112fa9f03b6:b565a85a493491c260acda69b780ef6ffa1cda87-0':
+        'biocontainers/mulled-v2-24c2519e6f79268102473627bccca112fa9f03b6:b565a85a493491c260acda69b780ef6ffa1cda87-0' }"
 
     input:
     tuple val(meta), path(fasta), path(fai)

modules/local/fishertest/main.nf

@@ -3,10 +3,9 @@ process FISHERTEST {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container 'fishbotherer/fishertest:1.0.2'
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    //     'https://depot.galaxyproject.org/singularity/mulled-v2-dd9299acb4f2a6af9c57792a648c9b309383d16a:006ebbae55f43556724857309229bb9ee9b5f648-0':
-    //     'biocontainers/mulled-v2-dd9299acb4f2a6af9c57792a648c9b309383d16a:006ebbae55f43556724857309229bb9ee9b5f648-0' }"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-91e4157032c00e9d9ac47f9837a67abee8f5afc2:7945c7dcdead60dfcbf06b19f4758634d6ad230a-0':
+        'biocontainers/mulled-v2-91e4157032c00e9d9ac47f9837a67abee8f5afc2:7945c7dcdead60dfcbf06b19f4758634d6ad230a-0' }"
 
     input:
     tuple val(meta), val(pools), path(frequency)

modules/local/joinfreq/main.nf

@@ -3,10 +3,9 @@ process JOINFREQ {
     label 'process_single_mem'
 
     conda "${moduleDir}/environment.yml"
-    container 'fishbotherer/fishertest:1.0.2'
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    //     'https://depot.galaxyproject.org/singularity/mulled-v2-1021c2bc41756fa99bc402f461dad0d1c35358c1:b0c847e4fb89c343b04036e33b2daa19c4152cf5-0':
-    //     'biocontainers/mulled-v2-1021c2bc41756fa99bc402f461dad0d1c35358c1:b0c847e4fb89c343b04036e33b2daa19c4152cf5-0' }"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-91e4157032c00e9d9ac47f9837a67abee8f5afc2:7945c7dcdead60dfcbf06b19f4758634d6ad230a-0':
+        'biocontainers/mulled-v2-91e4157032c00e9d9ac47f9837a67abee8f5afc2:7945c7dcdead60dfcbf06b19f4758634d6ad230a-0' }"
 
     input:
     tuple val(meta), path(frequency), path(fst), val(method)

modules/local/poolfstat/fst/main.nf

@@ -3,10 +3,9 @@ process POOLFSTAT_FST {
     label 'process_medium_low'
 
     conda "${moduleDir}/environment.yml"
-    container 'fishbotherer/poolfstat:1.0.2'
-    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    //     'https://depot.galaxyproject.org/singularity/mulled-v2-5d425a6e26ab032a4dcba5bc997f43ab9299830a:a1958d454debf3df6f397d04d5f094df68682ef9-0':
-    //     'biocontainers/mulled-v2-5d425a6e26ab032a4dcba5bc997f43ab9299830a:a1958d454debf3df6f397d04d5f094df68682ef9-0' }"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-618be27569d1bdadeed1044f0388638f6bfca2ae:095239e9e7e75cc2b7273c9a69167d844dd9b634-0':
+        'biocontainers/mulled-v2-618be27569d1bdadeed1044f0388638f6bfca2ae:095239e9e7e75cc2b7273c9a69167d844dd9b634-0' }"
 
     input:
     tuple val(meta), val(pool_map), path(sync)