Add functional Biocontainer

nf-core · Aug 2, 2023 · f81dfd9 · f81dfd9
1 parent ea20a1c
commit f81dfd9
Showing 1 changed file with 3 additions and 12 deletions.
diff --git a/modules/local/summary_report.nf b/modules/local/summary_report.nf
@@ -1,19 +1,10 @@
 process SUMMARY_REPORT  {
     label 'process_low'
 
-    container 'docker.io/tillenglert/ampliseq_report:latest'
-    /* this is from https://github.com/nf-core/modules/blob/master/modules/nf-core/rmarkdownnotebook/main.nf but doesnt work
-    conda "conda-forge::r-base=4.1.0 conda-forge::r-rmarkdown=2.9 conda-forge::r-yaml=2.2.1"
+    conda "conda-forge::r-base=4.2.3 conda-forge::r-rmarkdown=2.22 conda-forge::r-tidyverse=2.0.0 conda-forge::r-knitr=1.43 conda-forge::r-dt=0.28 conda-forge::r-dtplyr=1.3.1 conda-forge::r-formattable=0.2.1 conda-forge::r-purrr=1.0.1 conda-forge::r-vegan=2.6_4 conda-forge::r-optparse=1.7.3 conda-forge::r-ggplot2=3.4.2 conda-forge::r-dplyr=1.1.2 conda-forge::r-data.table=1.14.8 conda-forge::r-patchwork=1.1.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
-        'biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }"
-    */
-    /* this is from https://github.com/BioContainers/multi-package-containers/pull/2663 but doesnt work: /usr/local/bin/pandoc: error while loading shared libraries: libgmp.so.10: cannot open shared object file: No such file or directory
-    conda "conda-forge::r-base=4.2.3 conda-forge::r-rmarkdown=2.22 conda-forge::r-tidyverse=2.0.0 conda-forge::r-knitr=1.43 conda-forge::r-dt=0.28 conda-forge::r-dtplyr=1.3.1 conda-forge::r-formattable=0.2.1 conda-forge::r-purrr=1.0.1 conda-forge::r-vegan=2.6_4 conda-forge::r-optparse=1.7.3 conda-forge::r-ggplot2=3.4.2 conda-forge::r-dplyr=1.1.2 conda-forge::r-data.table=1.14.8 conda-forge::pandoc=2.19.2 conda-forge::r-patchwork=1.1.2"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-6726188ca70388ddb300400dc7fe71101a4f89f2:0346b3395cd017327aff8dae37aad0a027a7613c-0' :
-        'biocontainers/mulled-v2-6726188ca70388ddb300400dc7fe71101a4f89f2:0346b3395cd017327aff8dae37aad0a027a7613c-0' }"
-    */
+        'https://depot.galaxyproject.org/singularity/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' :
+        'biocontainers/mulled-v2-b2ec1fea5791d428eebb8c8ea7409c350d31dada:a447f6b7a6afde38352b24c30ae9cd6e39df95c4-1' }"
 
     input:
     path(report_template)