From 086468f887a1f21f3f38231d5a0309f132f42b36 Mon Sep 17 00:00:00 2001 From: Rainer Knoll <137690310+knollr@users.noreply.github.com> Date: Tue, 14 May 2024 16:31:59 +0200 Subject: [PATCH 1/7] add channel for samtools --- modules/multi/gene_demultiplexing.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/multi/gene_demultiplexing.nf b/modules/multi/gene_demultiplexing.nf index e2e5cf3..3bba3f3 100644 --- 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=19.2 bedtools bcftools=1.19" tag "${sampleId}" input: tuple val(sampleId), path(sam), path(sam_index), path(barcodes) From e18a476f9ca862e0748e9d256bb031f67022ad56 Mon Sep 17 00:00:00 2001 From: Rainer Knoll <137690310+knollr@users.noreply.github.com> Date: Tue, 14 May 2024 16:51:03 +0200 Subject: [PATCH 2/7] add channel for samtools --- modules/multi/gene_demulti/freemuxlet.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/multi/gene_demulti/freemuxlet.nf b/modules/multi/gene_demulti/freemuxlet.nf index 6d7f12e..c769177 100755 --- a/modules/multi/gene_demulti/freemuxlet.nf +++ b/modules/multi/gene_demulti/freemuxlet.nf @@ -4,7 +4,7 @@ nextflow.enable.dsl=2 process subset_bam_and_sort_vcf_based_on_reference{ label 'small_mem' - conda "bioconda::samtools=1.19.2 bedtools bcftools=1.19" + conda "-c conda-forge -c bioconda samtools=19.2 bedtools bcftools=1.19" tag "${sampleId}" input: tuple val(sampleId), path(sam), path(sam_index), path(group_list), val(nsample) From 15062d7057ded2eec121a3c229fdcc4749effac5 Mon Sep 17 00:00:00 2001 From: Rainer Knoll <137690310+knollr@users.noreply.github.com> Date: Tue, 14 May 2024 16:51:51 +0200 Subject: [PATCH 3/7] add channel for samtools --- modules/multi/gene_demulti/demuxlet.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/multi/gene_demulti/demuxlet.nf b/modules/multi/gene_demulti/demuxlet.nf index 0d33fcf..2405a3b 100755 --- 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=19.2 bedtools bcftools=1.19" tag "${sampleId}" input: tuple val(sampleId), path(sam), path(sam_index), path(barcodes), val(vcf) From 61dd0a14b444f62ccb7528ca8d1024c41063911d Mon Sep 17 00:00:00 2001 From: Rainer Knoll <137690310+knollr@users.noreply.github.com> Date: Tue, 14 May 2024 17:16:24 +0200 Subject: [PATCH 4/7] conda-forge for scanpy and muon --- modules/multi/gene_demultiplexing.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/multi/gene_demultiplexing.nf b/modules/multi/gene_demultiplexing.nf index 3bba3f3..26c4029 100644 --- a/modules/multi/gene_demultiplexing.nf +++ b/modules/multi/gene_demultiplexing.nf @@ -45,7 +45,7 @@ process summary{ publishDir "$params.outdir/$sampleId/$params.mode/gene_demulti", mode: 'copy' label 'small_mem' tag "${sampleId}" - conda "pandas scanpy mudata" + conda "-c conda-forge pandas scanpy mudata" input: tuple(val(sampleId), path(hto_matrix, stageAs: 'hto_data'), path(rna_matrix, stageAs: 'rna_data'), val(souporcell_result), val(scsplit_result), val(vireo_result),val(freemuxlet_result),val(demuxlet_result)) From 30e1200bca42dd7e1b4294761ce4c03d3bbbab77 Mon Sep 17 00:00:00 2001 From: Xichen Wu <102925032+wxicu@users.noreply.github.com> Date: Sat, 18 May 2024 16:09:42 +0200 Subject: [PATCH 5/7] fix version of samtools --- modules/multi/gene_demulti/demuxlet.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/multi/gene_demulti/demuxlet.nf b/modules/multi/gene_demulti/demuxlet.nf index 2405a3b..927702f 100755 --- a/modules/multi/gene_demulti/demuxlet.nf +++ b/modules/multi/gene_demulti/demuxlet.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl=2 process subset_bam_and_sort_vcf_based_on_reference{ label 'small_mem' - conda "-c conda-forge -c bioconda samtools=19.2 bedtools bcftools=1.19" + conda "-c conda-forge -c bioconda samtools=1.19.2 bedtools bcftools=1.19" tag "${sampleId}" input: tuple val(sampleId), path(sam), path(sam_index), path(barcodes), val(vcf) From c4d4405fc80710f16ae0a9739593e0c30afa1da2 Mon Sep 17 00:00:00 2001 From: Xichen Wu <102925032+wxicu@users.noreply.github.com> Date: Sat, 18 May 2024 16:10:08 +0200 Subject: [PATCH 6/7] fix version of samtools in freemuxlet --- modules/multi/gene_demulti/freemuxlet.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/multi/gene_demulti/freemuxlet.nf b/modules/multi/gene_demulti/freemuxlet.nf index c769177..fe5afdc 100755 --- 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 "-c conda-forge -c bioconda samtools=19.2 bedtools bcftools=1.19" + conda "-c conda-forge -c bioconda samtools=1.19.2 bedtools bcftools=1.19" tag "${sampleId}" input: tuple val(sampleId), path(sam), path(sam_index), path(group_list), val(nsample) From cae0b6050d57c513af1767ec1d0646b8ab8a09d7 Mon Sep 17 00:00:00 2001 From: Xichen Wu <102925032+wxicu@users.noreply.github.com> Date: Sat, 18 May 2024 16:10:44 +0200 Subject: [PATCH 7/7] fix version of samtools in script --- modules/multi/gene_demultiplexing.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/multi/gene_demultiplexing.nf b/modules/multi/gene_demultiplexing.nf index 26c4029..d1086a1 100644 --- a/modules/multi/gene_demultiplexing.nf +++ b/modules/multi/gene_demultiplexing.nf @@ -24,7 +24,7 @@ def split_input(input){ process subset_bam_to_comon_variants{ label 'small_mem' - conda "-c conda-forge -c bioconda samtools=19.2 bedtools bcftools=1.19" + conda "-c conda-forge -c bioconda samtools=1.19.2 bedtools bcftools=1.19" tag "${sampleId}" input: tuple val(sampleId), path(sam), path(sam_index), path(barcodes)