From 1fe8ac3d0613c7350c64a4dee87bf2ae0b093b34 Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 23 Apr 2021 16:33:42 +0200
Subject: [PATCH] Use biocontainers images for bedtools, bedgraphtobigwig,
cutadapt, kallisto, samtools, star, salmon, gffread. Partially fixes #149
---
Snakefile | 20 ++++++++++----------
workflow/rules/paired_end.snakefile.smk | 10 +++++-----
workflow/rules/single_end.snakefile.smk | 10 +++++-----
3 files changed, 20 insertions(+), 20 deletions(-)
diff --git a/Snakefile b/Snakefile
index 2f5842a..f0303c3 100644
--- a/Snakefile
+++ b/Snakefile
@@ -302,7 +302,7 @@ rule create_index_star:
)
singularity:
- "docker://zavolab/star:2.7.3a-slim"
+ "docker://quay.io/biocontainers/star:2.7.3a--0"
threads: 12
@@ -371,7 +371,7 @@ rule extract_transcriptome:
current_rule + "_{organism}.log")
singularity:
- "docker://zavolab/gffread:0.11.7-slim"
+ "docker://quay.io/biocontainers/gffread:0.11.7--h8b12597_0"
shell:
"(gffread \
@@ -462,7 +462,7 @@ rule create_index_salmon:
)
singularity:
- "docker://zavolab/salmon:1.1.0-slim"
+ "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
log:
stderr = os.path.join(
@@ -516,7 +516,7 @@ rule create_index_kallisto:
)
singularity:
- "docker://zavolab/kallisto:0.46.1-slim"
+ "docker://quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0"
log:
stderr = os.path.join(
@@ -609,7 +609,7 @@ rule index_genomic_alignment_samtools:
)
singularity:
- "docker://zavolab/samtools:1.10-slim"
+ "docker://quay.io/biocontainers/samtools:1.10--h2e538c0_3"
threads: 1
@@ -779,7 +779,7 @@ rule salmon_quantmerge_genes:
threads: 1
singularity:
- "docker://zavolab/salmon:1.1.0-slim"
+ "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
shell:
"(salmon quantmerge \
@@ -862,7 +862,7 @@ rule salmon_quantmerge_transcripts:
threads: 1
singularity:
- "docker://zavolab/salmon:1.1.0-slim"
+ "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
shell:
"(salmon quantmerge \
@@ -1208,7 +1208,7 @@ rule star_rpm:
)
singularity:
- "docker://zavolab/star:2.7.3a-slim"
+ "docker://quay.io/biocontainers/star:2.7.3a--0"
log:
stderr = os.path.join(
@@ -1674,7 +1674,7 @@ rule sort_bed_4_big:
)
singularity:
- "docker://cjh4zavolab/bedtools:2.27"
+ "docker://quay.io/biocontainers/bedtools:2.27.1--h9a82719_5"
log:
stderr = os.path.join(
@@ -1734,7 +1734,7 @@ rule prepare_bigWig:
)
singularity:
- "docker://zavolab/bedgraphtobigwig:4-slim"
+ "docker://quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h0b8a92a_2"
log:
stderr = os.path.join(
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 3f7834c..78d9937 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -53,7 +53,7 @@ rule pe_remove_adapters_cutadapt:
)
singularity:
- "docker://zavolab/cutadapt:1.16-slim"
+ "docker://quay.io/biocontainers/cutadapt:1.16--py35_2"
threads: 8
@@ -148,7 +148,7 @@ rule pe_remove_polya_cutadapt:
)
singularity:
- "docker://zavolab/cutadapt:1.16-slim"
+ "docker://quay.io/biocontainers/cutadapt:1.16--py35_2"
threads: 8
@@ -279,7 +279,7 @@ rule pe_map_genome_star:
)
singularity:
- "docker://zavolab/star:2.7.3a-slim"
+ "docker://quay.io/biocontainers/star:2.7.3a--0"
threads: 12
@@ -414,7 +414,7 @@ rule pe_quantification_salmon:
threads: 6
singularity:
- "docker://zavolab/salmon:1.1.0-slim"
+ "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
shell:
"(salmon quant \
@@ -498,7 +498,7 @@ rule pe_genome_quantification_kallisto:
singularity:
- "docker://zavolab/kallisto:0.46.1-slim"
+ "docker://quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0"
threads: 8
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 337ae75..ae6e01b 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -43,7 +43,7 @@ rule remove_adapters_cutadapt:
)
singularity:
- "docker://zavolab/cutadapt:1.16-slim"
+ "docker://quay.io/biocontainers/cutadapt:1.16--py35_2"
threads: 8
@@ -113,7 +113,7 @@ rule remove_polya_cutadapt:
)
singularity:
- "docker://zavolab/cutadapt:1.16-slim"
+ "docker://quay.io/biocontainers/cutadapt:1.16--py35_2"
threads: 8
@@ -223,7 +223,7 @@ rule map_genome_star:
)
singularity:
- "docker://zavolab/star:2.7.3a-slim"
+ "docker://quay.io/biocontainers/star:2.7.3a--0"
threads: 12
@@ -361,7 +361,7 @@ rule quantification_salmon:
threads: 12
singularity:
- "docker://zavolab/salmon:1.1.0-slim"
+ "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
shell:
"(salmon quant \
@@ -459,7 +459,7 @@ rule genome_quantification_kallisto:
current_rule + ".se.stderr.log")
singularity:
- "docker://zavolab/kallisto:0.46.1-slim"
+ "docker://quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0"
shell:
"(kallisto quant \
--
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