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Commit e265ed75 authored by BIOPZ-Gypas Foivos's avatar BIOPZ-Gypas Foivos
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Use biocontainers images for star, gffread, salmon, kallisto, cutadapt,... 

Use biocontainers images for star, gffread, salmon, kallisto, cutadapt, samtools, fastqc, alfa, bedtools, bedgraphtobigwig. Change container from bash to ubuntu. Fixes #149
parents 10e8891c be8eb02d
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1 merge request!84Biocontainer images
Pipeline #12400 passed
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View file @ e265ed75
...@@ -180,7 +180,7 @@ rule start: ...@@ -180,7 +180,7 @@ rule start:
current_rule + "_{sample}.{mate}.stdout.log") current_rule + "_{sample}.{mate}.stdout.log")
singularity: singularity:
"docker://bash:5.0.16" "docker://ubuntu:focal-20210416"
shell: shell:
"(cat {input.reads} > {output.reads}) \ "(cat {input.reads} > {output.reads}) \
...@@ -221,7 +221,7 @@ rule fastqc: ...@@ -221,7 +221,7 @@ rule fastqc:
threads: 2 threads: 2
singularity: singularity:
"docker://zavolab/fastqc:0.11.9-slim" "docker://quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1"
log: log:
stderr = os.path.join( stderr = os.path.join(
...@@ -302,7 +302,7 @@ rule create_index_star: ...@@ -302,7 +302,7 @@ rule create_index_star:
) )
singularity: singularity:
"docker://zavolab/star:2.7.3a-slim" "docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
threads: 12 threads: 12
...@@ -371,7 +371,7 @@ rule extract_transcriptome: ...@@ -371,7 +371,7 @@ rule extract_transcriptome:
current_rule + "_{organism}.log") current_rule + "_{organism}.log")
singularity: singularity:
"docker://zavolab/gffread:0.11.7-slim" "docker://quay.io/biocontainers/gffread:0.12.1--h2e03b76_1"
shell: shell:
"(gffread \ "(gffread \
...@@ -408,7 +408,7 @@ rule concatenate_transcriptome_and_genome: ...@@ -408,7 +408,7 @@ rule concatenate_transcriptome_and_genome:
"genome_transcriptome.fa")) "genome_transcriptome.fa"))
singularity: singularity:
"docker://bash:5.0.16" "docker://ubuntu:focal-20210416"
log: log:
stderr = os.path.join( stderr = os.path.join(
...@@ -462,7 +462,7 @@ rule create_index_salmon: ...@@ -462,7 +462,7 @@ rule create_index_salmon:
) )
singularity: singularity:
"docker://zavolab/salmon:1.1.0-slim" "docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
log: log:
stderr = os.path.join( stderr = os.path.join(
...@@ -516,7 +516,7 @@ rule create_index_kallisto: ...@@ -516,7 +516,7 @@ rule create_index_kallisto:
) )
singularity: singularity:
"docker://zavolab/kallisto:0.46.1-slim" "docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
log: log:
stderr = os.path.join( stderr = os.path.join(
...@@ -609,7 +609,7 @@ rule index_genomic_alignment_samtools: ...@@ -609,7 +609,7 @@ rule index_genomic_alignment_samtools:
) )
singularity: singularity:
"docker://zavolab/samtools:1.10-slim" "docker://quay.io/biocontainers/samtools:1.3.1--h1b8c3c0_8"
threads: 1 threads: 1
...@@ -779,7 +779,7 @@ rule salmon_quantmerge_genes: ...@@ -779,7 +779,7 @@ rule salmon_quantmerge_genes:
threads: 1 threads: 1
singularity: singularity:
"docker://zavolab/salmon:1.1.0-slim" "docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
shell: shell:
"(salmon quantmerge \ "(salmon quantmerge \
...@@ -862,7 +862,7 @@ rule salmon_quantmerge_transcripts: ...@@ -862,7 +862,7 @@ rule salmon_quantmerge_transcripts:
threads: 1 threads: 1
singularity: singularity:
"docker://zavolab/salmon:1.1.0-slim" "docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
shell: shell:
"(salmon quantmerge \ "(salmon quantmerge \
...@@ -1208,7 +1208,7 @@ rule star_rpm: ...@@ -1208,7 +1208,7 @@ rule star_rpm:
) )
singularity: singularity:
"docker://zavolab/star:2.7.3a-slim" "docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
log: log:
stderr = os.path.join( stderr = os.path.join(
...@@ -1298,7 +1298,7 @@ rule rename_star_rpm_for_alfa: ...@@ -1298,7 +1298,7 @@ rule rename_star_rpm_for_alfa:
current_rule + "_{unique}.stdout.log") current_rule + "_{unique}.stdout.log")
singularity: singularity:
"docker://bash:5.0.16" "docker://ubuntu:focal-20210416"
shell: shell:
"(cp {input.plus} {output.plus}; \ "(cp {input.plus} {output.plus}; \
...@@ -1354,7 +1354,7 @@ rule generate_alfa_index: ...@@ -1354,7 +1354,7 @@ rule generate_alfa_index:
threads: 4 threads: 4
singularity: singularity:
"docker://zavolab/alfa:1.1.1-slim" "docker://quay.io/biocontainers/alfa:1.1.1--pyh5e36f6f_0"
log: log:
os.path.join( os.path.join(
...@@ -1457,7 +1457,7 @@ rule alfa_qc: ...@@ -1457,7 +1457,7 @@ rule alfa_qc:
) )
singularity: singularity:
"docker://zavolab/alfa:1.1.1-slim" "docker://quay.io/biocontainers/alfa:1.1.1--pyh5e36f6f_0"
log: log:
os.path.join( os.path.join(
...@@ -1674,7 +1674,7 @@ rule sort_bed_4_big: ...@@ -1674,7 +1674,7 @@ rule sort_bed_4_big:
) )
singularity: singularity:
"docker://cjh4zavolab/bedtools:2.27" "docker://quay.io/biocontainers/bedtools:2.27.1--h9a82719_5"
log: log:
stderr = os.path.join( stderr = os.path.join(
...@@ -1734,7 +1734,7 @@ rule prepare_bigWig: ...@@ -1734,7 +1734,7 @@ rule prepare_bigWig:
) )
singularity: singularity:
"docker://zavolab/bedgraphtobigwig:4-slim" "docker://quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h0b8a92a_2"
log: log:
stderr = os.path.join( stderr = os.path.join(
......
tests/test_integration_workflow/expected_output.md5
+ 30
− 30
View file @ e265ed75
cbaebdb67aee4784b64aff7fec9fda42 results/kallisto_indexes/homo_sapiens/kallisto.idx 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 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 dee7cdc194d5d0617552b7a3b5ad8dfb results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
8e2e96e2d6b7f29940ad5de40662b7cb results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt 8e2e96e2d6b7f29940ad5de40662b7cb results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
d0826904b8afa45352906ad9591f2bfb results/star_indexes/homo_sapiens/75/STAR_index/chrName.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 ...@@ -11,7 +11,7 @@ bad9d837f9a988694cc7080ee6d2997a results/star_indexes/homo_sapiens/75/STAR_inde
0c0b013fb8cbb8f3cb7a7bf92f3b1544 results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab 0c0b013fb8cbb8f3cb7a7bf92f3b1544 results/star_indexes/homo_sapiens/75/STAR_index/geneInfo.tab
00dda17b3c3983873d1474e9a758d6e6 results/star_indexes/homo_sapiens/75/STAR_index/Genome 00dda17b3c3983873d1474e9a758d6e6 results/star_indexes/homo_sapiens/75/STAR_index/Genome
c0d91c3af633d9439bfd0160d11efe4d results/star_indexes/homo_sapiens/75/STAR_index/SA 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 bae93882f9148a6c55816b733c32a3a2 results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
875030141343fca11f0b5aa1a37e1b66 results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab 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 ea36f062eedc7f54ceffea2b635a25a8 results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab
...@@ -26,39 +26,39 @@ e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synt ...@@ -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 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 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 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 caf24c834f9f8aa31473c3d5826227ac 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 909c316306050c8f7dfb9ad72dfe0334 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 3f7d7acd0b42a4e3642f3cc8f81e7b8d 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
848396c145d2157f34bbf86757f51abe 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_quality.png 5475f0266800b9febf00979b8dc561e6 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_quality.png
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 42462f1beeecb7820682284f7d5518cf 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
e4c1a39967ec9547a2e4c71c97982ee0 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_gc_content.png dc6b69c56474f492bbc9824631ac84d3 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_gc_content.png
69b70e3f561b749bf10b186dd2480a8a results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_quality.png b5a5a126e3f85478abdac1074aaf2fe1 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_sequence_quality.png
b28aac49f537b8cba364b6422458ad28 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_tile_quality.png f399fa5792cdfb72fac7ae2226723122 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/per_tile_quality.png
5b950b5dfe3c7407e9aac153db330a38 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/sequence_length_distribution.png e342ab7fae5112b9ebca5a04cc6230a2 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/Images/sequence_length_distribution.png
310130cbb8bbb6517f37ea0ff6586d43 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/adapter_content.png caf24c834f9f8aa31473c3d5826227ac results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/adapter_content.png
42741852cc110a151580bb3bb5180fc0 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/duplication_levels.png 909c316306050c8f7dfb9ad72dfe0334 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/duplication_levels.png
8b34217d5fd931966d9007a658570e67 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_n_content.png 3f7d7acd0b42a4e3642f3cc8f81e7b8d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_n_content.png
848396c145d2157f34bbf86757f51abe results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_quality.png 5475f0266800b9febf00979b8dc561e6 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_base_quality.png
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b28aac49f537b8cba364b6422458ad28 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_tile_quality.png f399fa5792cdfb72fac7ae2226723122 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_tile_quality.png
5b950b5dfe3c7407e9aac153db330a38 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/sequence_length_distribution.png e342ab7fae5112b9ebca5a04cc6230a2 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/sequence_length_distribution.png
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.kallisto.pseudo.sam d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.kallisto.pseudo.sam
500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_adapters_mate1.fastq 500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_adapters_mate1.fastq
500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_polya_mate1.fastq 500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.remove_polya_mate1.fastq
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tests/test_integration_workflow_multiple_lanes/expected_output.md5
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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 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 3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index 6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
......
workflow/rules/paired_end.snakefile.smk
+ 5
− 5
View file @ e265ed75
...@@ -53,7 +53,7 @@ rule pe_remove_adapters_cutadapt: ...@@ -53,7 +53,7 @@ rule pe_remove_adapters_cutadapt:
) )
singularity: singularity:
"docker://zavolab/cutadapt:1.16-slim" "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
threads: 8 threads: 8
...@@ -148,7 +148,7 @@ rule pe_remove_polya_cutadapt: ...@@ -148,7 +148,7 @@ rule pe_remove_polya_cutadapt:
) )
singularity: singularity:
"docker://zavolab/cutadapt:1.16-slim" "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
threads: 8 threads: 8
...@@ -279,7 +279,7 @@ rule pe_map_genome_star: ...@@ -279,7 +279,7 @@ rule pe_map_genome_star:
) )
singularity: singularity:
"docker://zavolab/star:2.7.3a-slim" "docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
threads: 12 threads: 12
...@@ -414,7 +414,7 @@ rule pe_quantification_salmon: ...@@ -414,7 +414,7 @@ rule pe_quantification_salmon:
threads: 6 threads: 6
singularity: singularity:
"docker://zavolab/salmon:1.1.0-slim" "docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
shell: shell:
"(salmon quant \ "(salmon quant \
...@@ -498,7 +498,7 @@ rule pe_genome_quantification_kallisto: ...@@ -498,7 +498,7 @@ rule pe_genome_quantification_kallisto:
singularity: singularity:
"docker://zavolab/kallisto:0.46.1-slim" "docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
threads: 8 threads: 8
......
workflow/rules/single_end.snakefile.smk
+ 6
− 6
View file @ e265ed75
...@@ -43,7 +43,7 @@ rule remove_adapters_cutadapt: ...@@ -43,7 +43,7 @@ rule remove_adapters_cutadapt:
) )
singularity: singularity:
"docker://zavolab/cutadapt:1.16-slim" "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
threads: 8 threads: 8
...@@ -113,7 +113,7 @@ rule remove_polya_cutadapt: ...@@ -113,7 +113,7 @@ rule remove_polya_cutadapt:
) )
singularity: singularity:
"docker://zavolab/cutadapt:1.16-slim" "docker://quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1"
threads: 8 threads: 8
...@@ -223,7 +223,7 @@ rule map_genome_star: ...@@ -223,7 +223,7 @@ rule map_genome_star:
) )
singularity: singularity:
"docker://zavolab/star:2.7.3a-slim" "docker://quay.io/biocontainers/star:2.7.8a--h9ee0642_1"
threads: 12 threads: 12
...@@ -236,7 +236,7 @@ rule map_genome_star: ...@@ -236,7 +236,7 @@ rule map_genome_star:
shell: shell:
"(STAR \ "(STAR \
-- twopassMode {params.pass_mode} \ --twopassMode {params.pass_mode} \
--runThreadN {threads} \ --runThreadN {threads} \
--genomeDir {params.index} \ --genomeDir {params.index} \
--readFilesIn {input.reads} \ --readFilesIn {input.reads} \
...@@ -361,7 +361,7 @@ rule quantification_salmon: ...@@ -361,7 +361,7 @@ rule quantification_salmon:
threads: 12 threads: 12
singularity: singularity:
"docker://zavolab/salmon:1.1.0-slim" "docker://quay.io/biocontainers/salmon:1.4.0--h84f40af_1"
shell: shell:
"(salmon quant \ "(salmon quant \
...@@ -459,7 +459,7 @@ rule genome_quantification_kallisto: ...@@ -459,7 +459,7 @@ rule genome_quantification_kallisto:
current_rule + ".se.stderr.log") current_rule + ".se.stderr.log")
singularity: singularity:
"docker://zavolab/kallisto:0.46.1-slim" "docker://quay.io/biocontainers/kallisto:0.46.2--h60f4f9f_2"
shell: shell:
"(kallisto quant \ "(kallisto quant \
......
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