fix conda

d4straub · d4straub · commit b72340aa4205 · 2025-09-19T15:03:14.000+02:00
diff --git a/modules/local/assignsh.nf b/modules/local/assignsh.nf
@@ -2,7 +2,7 @@ process ASSIGNSH {
     tag "${asvtable}"
     label 'process_low'
 
-    conda "conda-forge::pandas=1.1.5"
+    conda "conda-forge::pandas=1.1.5 conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5':
         'biocontainers/pandas:1.1.5' }"
diff --git a/modules/local/barrnapsummary.nf b/modules/local/barrnapsummary.nf
@@ -1,7 +1,7 @@
 process BARRNAPSUMMARY {
     label 'process_single'
 
-    conda "conda-forge::python=3.9"
+    conda "conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9' :
         'biocontainers/python:3.9' }"
diff --git a/modules/local/combine_table.nf b/modules/local/combine_table.nf
@@ -1,7 +1,7 @@
 process COMBINE_TABLE {
     label 'process_low'
 
-    conda "bioconda::bioconductor-biostrings=2.58.0"
+    conda "bioconda::bioconductor-biostrings=2.58.0 conda-forge::r-base=4.0.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' :
         'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
diff --git a/modules/local/cutadapt_summary_merge.nf b/modules/local/cutadapt_summary_merge.nf
@@ -2,7 +2,7 @@ process CUTADAPT_SUMMARY_MERGE {
     tag "${files}"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/dada2_addspecies.nf b/modules/local/dada2_addspecies.nf
@@ -3,7 +3,7 @@ process DADA2_ADDSPECIES {
     label 'process_high'
     label 'single_cpu'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/dada2_denoising.nf b/modules/local/dada2_denoising.nf
@@ -3,7 +3,7 @@ process DADA2_DENOISING {
     label 'process_medium'
     label 'process_long'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/dada2_err.nf b/modules/local/dada2_err.nf
@@ -2,7 +2,7 @@ process DADA2_ERR {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/dada2_filtntrim.nf b/modules/local/dada2_filtntrim.nf
@@ -2,7 +2,7 @@ process DADA2_FILTNTRIM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/dada2_quality.nf b/modules/local/dada2_quality.nf
@@ -2,7 +2,7 @@ process DADA2_QUALITY {
     tag "$meta"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/dada2_rmchimera.nf b/modules/local/dada2_rmchimera.nf
@@ -2,7 +2,7 @@ process DADA2_RMCHIMERA {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/dada2_stats.nf b/modules/local/dada2_stats.nf
@@ -2,7 +2,7 @@ process DADA2_STATS {
     tag "$meta.run"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/dada2_taxonomy.nf b/modules/local/dada2_taxonomy.nf
@@ -2,7 +2,7 @@ process DADA2_TAXONOMY {
     tag "${fasta},${database}"
     label 'process_high'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/filter_clusters.nf b/modules/local/filter_clusters.nf
@@ -2,7 +2,7 @@ process FILTER_CLUSTERS {
     tag "${meta.id}"
     label 'process_low'
 
-    conda "conda-forge::pandas=1.1.5"
+    conda "conda-forge::pandas=1.1.5 conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5':
         'biocontainers/pandas:1.1.5' }"
diff --git a/modules/local/filter_codons.nf b/modules/local/filter_codons.nf
@@ -2,7 +2,7 @@ process FILTER_CODONS {
     tag "${fasta}"
     label 'process_low'
 
-    conda "conda-forge::pandas=1.1.5"
+    conda "conda-forge::pandas=1.1.5 conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5':
         'biocontainers/pandas:1.1.5' }"
diff --git a/modules/local/filter_len.nf b/modules/local/filter_len.nf
@@ -2,7 +2,7 @@ process FILTER_LEN {
     tag "${fasta}"
     label 'process_low'
 
-    conda "bioconda::bioconductor-biostrings=2.58.0"
+    conda "bioconda::bioconductor-biostrings=2.58.0 conda-forge::r-base=4.0.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' :
         'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
diff --git a/modules/local/filter_ssu.nf b/modules/local/filter_ssu.nf
@@ -2,7 +2,7 @@ process FILTER_SSU {
     tag "${fasta}"
     label 'process_low'
 
-    conda "bioconda::bioconductor-biostrings=2.58.0"
+    conda "bioconda::bioconductor-biostrings=2.58.0 conda-forge::r-base=4.0.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' :
         'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
diff --git a/modules/local/filter_stats.nf b/modules/local/filter_stats.nf
@@ -1,7 +1,7 @@
 process FILTER_STATS {
     label 'process_low'
 
-    conda "conda-forge::pandas=1.1.5"
+    conda "conda-forge::pandas=1.1.5 conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
         'biocontainers/pandas:1.1.5' }"
diff --git a/modules/local/format_pplacetax.nf b/modules/local/format_pplacetax.nf
@@ -2,7 +2,7 @@ process FORMAT_PPLACETAX {
     tag "${tax.baseName}"
     label 'process_high'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/format_taxonomy.nf b/modules/local/format_taxonomy.nf
@@ -28,7 +28,7 @@ process FORMAT_TAXONOMY {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(bash --version | sed -n 1p | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')
+        sed: \$(sed --version 2>&1 | sed -n 1p | sed 's/sed (GNU sed) //')
     END_VERSIONS
     """
 }
diff --git a/modules/local/format_taxonomy_qiime.nf b/modules/local/format_taxonomy_qiime.nf
@@ -28,7 +28,7 @@ process FORMAT_TAXONOMY_QIIME {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(bash --version | sed -n 1p | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')
+        sed: \$(sed --version 2>&1 | sed -n 1p | sed 's/sed (GNU sed) //')
     END_VERSIONS
     """
 }
diff --git a/modules/local/format_taxonomy_sidle.nf b/modules/local/format_taxonomy_sidle.nf
@@ -30,7 +30,7 @@ process FORMAT_TAXONOMY_SIDLE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(bash --version | sed -n 1p | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')
+        sed: \$(sed --version 2>&1 | sed -n 1p | sed 's/sed (GNU sed) //')
     END_VERSIONS
     """
 }
diff --git a/modules/local/format_taxonomy_sintax.nf b/modules/local/format_taxonomy_sintax.nf
@@ -26,7 +26,7 @@ process FORMAT_TAXONOMY_SINTAX {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(bash --version | sed -n 1p | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')
+        sed: \$(sed --version 2>&1 | sed -n 1p | sed 's/sed (GNU sed) //')
     END_VERSIONS
     """
 }
diff --git a/modules/local/format_taxresults.nf b/modules/local/format_taxresults.nf
@@ -1,7 +1,7 @@
 process FORMAT_TAXRESULTS {
     label 'process_low'
 
-    conda "conda-forge::pandas=1.1.5"
+    conda "conda-forge::pandas=1.1.5 conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
         'biocontainers/pandas:1.1.5' }"
diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf
@@ -1,7 +1,7 @@
 process MERGE_STATS {
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/metadata_all.nf b/modules/local/metadata_all.nf
@@ -2,7 +2,7 @@ process METADATA_ALL {
     tag "$metadata"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/metadata_pairwise.nf b/modules/local/metadata_pairwise.nf
@@ -2,7 +2,7 @@ process METADATA_PAIRWISE {
     tag "$metadata"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/novaseq_err.nf b/modules/local/novaseq_err.nf
@@ -2,7 +2,7 @@ process NOVASEQ_ERR {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.30.0"
+    conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
         'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
diff --git a/modules/local/phyloseq.nf b/modules/local/phyloseq.nf
@@ -2,7 +2,7 @@ process PHYLOSEQ {
     tag "$prefix"
     label 'process_low'
 
-    conda "bioconda::bioconductor-phyloseq=1.46.0"
+    conda "bioconda::bioconductor-phyloseq=1.46.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-phyloseq:1.46.0--r43hdfd78af_0' :
         'biocontainers/bioconductor-phyloseq:1.46.0--r43hdfd78af_0' }"
diff --git a/modules/local/phyloseq_inasv.nf b/modules/local/phyloseq_inasv.nf
@@ -19,7 +19,7 @@ process PHYLOSEQ_INASV {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bash: \$(bash --version | sed -n 1p | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')
+        sed: \$(sed --version 2>&1 | sed -n 1p | sed 's/sed (GNU sed) //')
     END_VERSIONS
     """
 }
diff --git a/modules/local/phyloseq_intax.nf b/modules/local/phyloseq_intax.nf
@@ -1,7 +1,7 @@
 process PHYLOSEQ_INTAX {
     label 'process_low'
 
-    conda "conda-forge::pandas=1.1.5"
+    conda "conda-forge::pandas=1.1.5 conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5':
         'biocontainers/pandas:1.1.5' }"
diff --git a/modules/local/treesummarizedexperiment.nf b/modules/local/treesummarizedexperiment.nf
@@ -2,7 +2,7 @@ process TREESUMMARIZEDEXPERIMENT {
     tag "$prefix"
     label 'process_low'
 
-    conda "bioconda::bioconductor-treesummarizedexperiment=2.10.0"
+    conda "bioconda::bioconductor-treesummarizedexperiment=2.10.0 conda-forge::r-base=4.3.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-treesummarizedexperiment:2.10.0--r43hdfd78af_0' :
         'biocontainers/bioconductor-treesummarizedexperiment:2.10.0--r43hdfd78af_0' }"
diff --git a/modules/local/trunclen.nf b/modules/local/trunclen.nf
@@ -2,7 +2,7 @@ process TRUNCLEN {
     tag "$meta"
     label 'process_low'
 
-    conda "conda-forge::pandas=1.1.5"
+    conda "conda-forge::pandas=1.1.5 conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
         'biocontainers/pandas:1.1.5' }"
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
diff --git a/tests/fasta.nf.test.snap b/tests/fasta.nf.test.snap
diff --git a/tests/iontorrent.nf.test.snap b/tests/iontorrent.nf.test.snap
diff --git a/tests/multi.nf.test.snap b/tests/multi.nf.test.snap
diff --git a/tests/multiregion.nf.test.snap b/tests/multiregion.nf.test.snap
diff --git a/tests/pacbio_its.nf.test.snap b/tests/pacbio_its.nf.test.snap
diff --git a/tests/single.nf.test.snap b/tests/single.nf.test.snap
diff --git a/tests/sintax.nf.test.snap b/tests/sintax.nf.test.snap
