Merge pull request #52 from knollr/patch-1

add conda channels for samtools, scanpy, muon
theislab · May 18, 2024 · a90bb7c · a90bb7c
2 parents 6441e66 + cae0b60
commit a90bb7c
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/modules/multi/gene_demulti/demuxlet.nf b/modules/multi/gene_demulti/demuxlet.nf
@@ -5,7 +5,7 @@ nextflow.enable.dsl=2
 
 process subset_bam_and_sort_vcf_based_on_reference{
     label 'small_mem'
-    conda "bioconda::samtools=1.19.2 bedtools bcftools=1.19"
+    conda "-c conda-forge -c bioconda samtools=1.19.2 bedtools bcftools=1.19"
     tag "${sampleId}"
     input:
         tuple val(sampleId), path(sam), path(sam_index), path(barcodes), val(vcf)

diff --git a/modules/multi/gene_demulti/freemuxlet.nf b/modules/multi/gene_demulti/freemuxlet.nf
@@ -4,7 +4,7 @@ nextflow.enable.dsl=2
 
 process subset_bam_and_sort_vcf_based_on_reference{
     label 'small_mem'
-    conda "bioconda::samtools=1.19.2 bedtools bcftools=1.19"
+    conda "-c conda-forge -c bioconda samtools=1.19.2 bedtools bcftools=1.19"
     tag "${sampleId}"
     input:
         tuple val(sampleId), path(sam), path(sam_index), path(group_list), val(nsample)

diff --git a/modules/multi/gene_demultiplexing.nf b/modules/multi/gene_demultiplexing.nf
@@ -24,7 +24,7 @@ def split_input(input){
 process subset_bam_to_comon_variants{
 
     label 'small_mem'
-    conda "bioconda::samtools=1.19.2 bedtools bcftools=1.19"
+    conda "-c conda-forge -c bioconda samtools=1.19.2 bedtools bcftools=1.19"
     tag "${sampleId}"
     input:
         tuple val(sampleId), path(sam), path(sam_index), path(barcodes)
@@ -45,7 +45,7 @@ process summary{
     publishDir "$params.outdir/$sampleId/$params.mode/gene_demulti", mode: 'copy'
     label 'small_mem'
     tag "${sampleId}"
-    conda "pandas scanpy mudata"
+    conda "-c conda-forge pandas scanpy mudata"
 
     input:
         tuple(val(sampleId), path(hto_matrix, stageAs: 'hto_data'), path(rna_matrix, stageAs: 'rna_data'), val(souporcell_result), val(scsplit_result), val(vireo_result),val(freemuxlet_result),val(demuxlet_result))