From be8eb02db4b28724b18f58570163835f1195ffb9 Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 7 May 2021 15:12:01 +0000
Subject: [PATCH] Use biocontainers images for star, gffread, salmon, kallisto,
cutadapt, samtools, fastqc, alfa, bedtools, bedgraphtobigwig. Change
container from bash to ubuntu. Fixes #149
---
Snakefile | 32 +++++-----
.../expected_output.md5 | 60 +++++++++----------
.../expected_output.md5 | 60 +++++++++----------
workflow/rules/paired_end.snakefile.smk | 10 ++--
workflow/rules/single_end.snakefile.smk | 12 ++--
5 files changed, 87 insertions(+), 87 deletions(-)
diff --git a/Snakefile b/Snakefile
index 2f5842a..588af36 100644
--- a/Snakefile
+++ b/Snakefile
@@ -180,7 +180,7 @@ rule start:
current_rule + "_{sample}.{mate}.stdout.log")
singularity:
- "docker://bash:5.0.16"
+ "docker://ubuntu:focal-20210416"
shell:
"(cat {input.reads} > {output.reads}) \
@@ -221,7 +221,7 @@ rule fastqc:
threads: 2
singularity:
- "docker://zavolab/fastqc:0.11.9-slim"
+ "docker://quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1"
log:
stderr = os.path.join(
@@ -302,7 +302,7 @@ rule create_index_star:
)
singularity:
- "docker://zavolab/star:2.7.3a-slim"
+ "docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
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:0.12.1--h2e03b76_1"
shell:
"(gffread \
@@ -408,7 +408,7 @@ rule concatenate_transcriptome_and_genome:
"genome_transcriptome.fa"))
singularity:
- "docker://bash:5.0.16"
+ "docker://ubuntu:focal-20210416"
log:
stderr = os.path.join(
@@ -462,7 +462,7 @@ rule create_index_salmon:
)
singularity:
- "docker://zavolab/salmon:1.1.0-slim"
+ "docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
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:0.46.2--h60f4f9f_2"
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:1.3.1--h1b8c3c0_8"
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:1.4.0--h84f40af_1"
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:1.4.0--h84f40af_1"
shell:
"(salmon quantmerge \
@@ -1208,7 +1208,7 @@ rule star_rpm:
)
singularity:
- "docker://zavolab/star:2.7.3a-slim"
+ "docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
log:
stderr = os.path.join(
@@ -1298,7 +1298,7 @@ rule rename_star_rpm_for_alfa:
current_rule + "_{unique}.stdout.log")
singularity:
- "docker://bash:5.0.16"
+ "docker://ubuntu:focal-20210416"
shell:
"(cp {input.plus} {output.plus}; \
@@ -1354,7 +1354,7 @@ rule generate_alfa_index:
threads: 4
singularity:
- "docker://zavolab/alfa:1.1.1-slim"
+ "docker://quay.io/biocontainers/alfa:1.1.1--pyh5e36f6f_0"
log:
os.path.join(
@@ -1457,7 +1457,7 @@ rule alfa_qc:
)
singularity:
- "docker://zavolab/alfa:1.1.1-slim"
+ "docker://quay.io/biocontainers/alfa:1.1.1--pyh5e36f6f_0"
log:
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/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index 4093ded..266f992 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -1,7 +1,7 @@
cbaebdb67aee4784b64aff7fec9fda42 results/kallisto_indexes/homo_sapiens/kallisto.idx
-0ac1afd9a4f380afd70be75b21814c64 results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
+204865f645102587c4953fccb256797c results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
51b5292e3a874119c0e1aa566e95d70c results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
-7f8679a6e6622e1b611642b5735f357c results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
+4e10114bb8f9096d594776181424a302 results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
dee7cdc194d5d0617552b7a3b5ad8dfb results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
8e2e96e2d6b7f29940ad5de40662b7cb results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
d0826904b8afa45352906ad9591f2bfb results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt
@@ -11,7 +11,7 @@ bad9d837f9a988694cc7080ee6d2997a results/star_indexes/homo_sapiens/75/STAR_inde
0c0b013fb8cbb8f3cb7a7bf92f3b1544 results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab
00dda17b3c3983873d1474e9a758d6e6 results/star_indexes/homo_sapiens/75/STAR_index/Genome
c0d91c3af633d9439bfd0160d11efe4d results/star_indexes/homo_sapiens/75/STAR_index/SA
-27884e419e42a7c8b3b2f49543de0260 results/star_indexes/homo_sapiens/75/STAR_index/SAindex
+a8dfc49713c053a8a1a2cc2527f15186 results/star_indexes/homo_sapiens/75/STAR_index/SAindex
bae93882f9148a6c55816b733c32a3a2 results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
875030141343fca11f0b5aa1a37e1b66 results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
ea36f062eedc7f54ceffea2b635a25a8 results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
@@ -26,39 +26,39 @@ e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synt
c39fc9108e6f6c0df45acc9391daad9c results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc_data.txt
82c37e4cb9c1e167383d589ccb5c80b4 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc.fo
2029b1ecea0c5fb3c54238813cf02a26 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/summary.txt
-310130cbb8bbb6517f37ea0ff6586d43 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/adapter_content.png
-42741852cc110a151580bb3bb5180fc0 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/duplication_levels.png
-8b34217d5fd931966d9007a658570e67 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_n_content.png
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-56bd6a5f95196121173609eb70618166 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_base_sequence_content.png
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d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.kallisto.pseudo.sam
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
diff --git a/tests/test_integration_workflow_multiple_lanes/expected_output.md5 b/tests/test_integration_workflow_multiple_lanes/expected_output.md5
index 1f2ce96..37f1119 100644
--- a/tests/test_integration_workflow_multiple_lanes/expected_output.md5
+++ b/tests/test_integration_workflow_multiple_lanes/expected_output.md5
@@ -1,7 +1,7 @@
cbaebdb67aee4784b64aff7fec9fda42 results/kallisto_indexes/homo_sapiens/kallisto.idx
-0ac1afd9a4f380afd70be75b21814c64 results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
+204865f645102587c4953fccb256797c results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
51b5292e3a874119c0e1aa566e95d70c results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
-7f8679a6e6622e1b611642b5735f357c results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
+4e10114bb8f9096d594776181424a302 results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
dee7cdc194d5d0617552b7a3b5ad8dfb results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
8e2e96e2d6b7f29940ad5de40662b7cb results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
d0826904b8afa45352906ad9591f2bfb results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt
@@ -11,7 +11,7 @@ bad9d837f9a988694cc7080ee6d2997a results/star_indexes/homo_sapiens/75/STAR_inde
0c0b013fb8cbb8f3cb7a7bf92f3b1544 results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab
00dda17b3c3983873d1474e9a758d6e6 results/star_indexes/homo_sapiens/75/STAR_index/Genome
c0d91c3af633d9439bfd0160d11efe4d results/star_indexes/homo_sapiens/75/STAR_index/SA
-27884e419e42a7c8b3b2f49543de0260 results/star_indexes/homo_sapiens/75/STAR_index/SAindex
+a8dfc49713c053a8a1a2cc2527f15186 results/star_indexes/homo_sapiens/75/STAR_index/SAindex
bae93882f9148a6c55816b733c32a3a2 results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
875030141343fca11f0b5aa1a37e1b66 results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab
ea36f062eedc7f54ceffea2b635a25a8 results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
@@ -26,39 +26,39 @@ e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synt
c39fc9108e6f6c0df45acc9391daad9c results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc_data.txt
82c37e4cb9c1e167383d589ccb5c80b4 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/fastqc.fo
2029b1ecea0c5fb3c54238813cf02a26 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/summary.txt
-310130cbb8bbb6517f37ea0ff6586d43 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/adapter_content.png
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3cb70940acdcca512207bd8613085538 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/fastqc/fq1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.fq1_fastqc/fastqc.fo
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d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.kallisto.pseudo.sam
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 3f7834c..0fc0d6b 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:3.4--py37h73a75cf_1"
threads: 8
@@ -148,7 +148,7 @@ rule pe_remove_polya_cutadapt:
)
singularity:
- "docker://zavolab/cutadapt:1.16-slim"
+ "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
threads: 8
@@ -279,7 +279,7 @@ rule pe_map_genome_star:
)
singularity:
- "docker://zavolab/star:2.7.3a-slim"
+ "docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
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:1.4.0--h84f40af_1"
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:0.46.2--h60f4f9f_2"
threads: 8
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 337ae75..c60cfb5 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:3.4--py37h73a75cf_1"
threads: 8
@@ -113,7 +113,7 @@ rule remove_polya_cutadapt:
)
singularity:
- "docker://zavolab/cutadapt:1.16-slim"
+ "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
threads: 8
@@ -223,7 +223,7 @@ rule map_genome_star:
)
singularity:
- "docker://zavolab/star:2.7.3a-slim"
+ "docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
threads: 12
@@ -236,7 +236,7 @@ rule map_genome_star:
shell:
"(STAR \
- -- twopassMode {params.pass_mode} \
+ --twopassMode {params.pass_mode} \
--runThreadN {threads} \
--genomeDir {params.index} \
--readFilesIn {input.reads} \
@@ -361,7 +361,7 @@ rule quantification_salmon:
threads: 12
singularity:
- "docker://zavolab/salmon:1.1.0-slim"
+ "docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
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:0.46.2--h60f4f9f_2"
shell:
"(kallisto quant \
--
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