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Commit dc2afcf9 authored by Alex Kanitz's avatar Alex Kanitz
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Use minified docker images

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Snakefile
+ 4
− 4
View file @ dc2afcf9
......@@ -148,7 +148,7 @@ rule create_index_star:
),
sjdbOverhang = "{index_size}",
singularity:
"docker://zavolab/star:2.6.0a"
"docker://zavolab/star:2.7.3a-slim"
threads: 12
log:
os.path.join(
......@@ -221,7 +221,7 @@ rule create_index_kallisto:
"{organism}",
),
singularity:
"docker://zavolab/kallisto:0.46.1"
"docker://zavolab/kallisto:0.46.1-slim"
log:
os.path.join(
config['log_dir'],
......@@ -244,7 +244,7 @@ rule extract_transcripts_as_bed12:
"full_transcripts_protein_coding.bed",
),
singularity:
"docker://zavolab/gtf_transcript_type_to_bed12:0.1.0"
"docker://zavolab/gtf_transcript_type_to_bed12:0.1.0-slim"
threads: 1
log:
os.path.join(
......@@ -299,7 +299,7 @@ rule calculate_TIN_scores:
)
threads: 8
singularity:
"docker://zavolab/tin_score_calculation:0.1.0"
"docker://zavolab/tin_score_calculation:0.1.0-slim"
shell:
"tin_score_calculation.py \
-i {params.bam} \
......
images/dag_test_workflow.svg
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− 420
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images/rule_graph.svg
+ 275
− 181
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This diff is collapsed.
tests/test_integration_workflow/expected_output.md5
+ 9
− 9
View file @ dc2afcf9
......@@ -8,23 +8,23 @@ d0826904b8afa45352906ad9591f2bfb results/star_indexes/homo_sapiens/75/STAR_inde
8d3291e6bcdbe9902fbd7c887494173f results/star_indexes/homo_sapiens/75/STAR_index/chrStart.txt
83ea3c15ab782b5c55bfaefda8e7aad8 results/star_indexes/homo_sapiens/75/STAR_index/exonGeTrInfo.tab
bad9d837f9a988694cc7080ee6d2997a results/star_indexes/homo_sapiens/75/STAR_index/exonInfo.tab
97e90abd8df5b91bd0b0f94dbeb66fbd 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
c0d91c3af633d9439bfd0160d11efe4d results/star_indexes/homo_sapiens/75/STAR_index/SA
27884e419e42a7c8b3b2f49543de0260 results/star_indexes/homo_sapiens/75/STAR_index/SAindex
bae93882f9148a6c55816b733c32a3a2 results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt
ea36f062eedc7f54ceffea2b635a25a8 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
59c4082523c0279740fa0452871dea4b results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
65e794aa5096551254af18a678d02264 results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab
500dd49da40b16799aba62aa5cf239ba results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate1.fastq
e90e31db1ce51d930645eb74ff70d21b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_adapters_mate2.fastq
500dd49da40b16799aba62aa5cf239ba results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate1.fastq
e90e31db1ce51d930645eb74ff70d21b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.remove_polya_mate2.fastq
d41d8cd98f00b204e9800998ecf8427e results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired_SJ.out.tab
69042457ef7ec3f401153e8503408ad4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
6c5d2ffd046e24384a7557aa9be0fdfd results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
c0df759ceab72ea4b1a560f991fe6497 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
a7530faae728593900da23fca4bea97a results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
fe6c1c9343d91f5413c8319ccd72b5d5 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
310130cbb8bbb6517f37ea0ff6586d43 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
42741852cc110a151580bb3bb5180fc0 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
8b34217d5fd931966d9007a658570e67 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_n_content.png
848396c145d2157f34bbf86757f51abe results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_quality.png
......@@ -33,10 +33,10 @@ e4c1a39967ec9547a2e4c71c97982ee0 results/paired_end/synthetic_10_reads_paired_s
69b70e3f561b749bf10b186dd2480a8a results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_sequence_quality.png
b28aac49f537b8cba364b6422458ad28 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_tile_quality.png
5b950b5dfe3c7407e9aac153db330a38 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate1_fastqc/synthetic.mate_1_fastqc/Images/sequence_length_distribution.png
9273c891e47c90fed47554fe8d1e706c results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc_data.txt
81ffdfa5e3d8b1e8984f15359b6306f7 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc_data.txt
5d406428979b59abf760b9be8b1877e2 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/fastqc.fo
706b6812d0313b6858e80a4e6aff453e results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/summary.txt
fe6c1c9343d91f5413c8319ccd72b5d5 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/adapter_content.png
310130cbb8bbb6517f37ea0ff6586d43 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/adapter_content.png
42741852cc110a151580bb3bb5180fc0 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/duplication_levels.png
8b34217d5fd931966d9007a658570e67 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_n_content.png
848396c145d2157f34bbf86757f51abe results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/mate2_fastqc/synthetic.mate_2_fastqc/Images/per_base_quality.png
......@@ -57,10 +57,10 @@ d41d8cd98f00b204e9800998ecf8427e results/paired_end/synthetic_10_reads_paired_s
12ac6d56ed50ab74ce16a4d618612847 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.remove_adapters_mate1.fastq
12ac6d56ed50ab74ce16a4d618612847 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.remove_polya_mate1.fastq
d41d8cd98f00b204e9800998ecf8427e results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_SJ.out.tab
69042457ef7ec3f401153e8503408ad4 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
6c5d2ffd046e24384a7557aa9be0fdfd results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc_data.txt
c0df759ceab72ea4b1a560f991fe6497 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/fastqc.fo
a7530faae728593900da23fca4bea97a results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/summary.txt
fe6c1c9343d91f5413c8319ccd72b5d5 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
310130cbb8bbb6517f37ea0ff6586d43 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/adapter_content.png
42741852cc110a151580bb3bb5180fc0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/duplication_levels.png
8b34217d5fd931966d9007a658570e67 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_n_content.png
848396c145d2157f34bbf86757f51abe results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/mate1_fastqc/synthetic.mate_1_fastqc/Images/per_base_quality.png
......
tests/test_integration_workflow/test.local.sh
+ 1
− 0
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......@@ -3,6 +3,7 @@
# Tear down test environment
cleanup () {
rc=$?
rm -rf .fontconfig/
rm -rf .java/
rm -rf .snakemake/
rm -rf logs/
......
tests/test_integration_workflow/test.slurm.sh
+ 1
− 0
View file @ dc2afcf9
......@@ -3,6 +3,7 @@
# Tear down test environment
cleanup () {
rc=$?
rm -rf .fontconfig/
rm -rf .java/
rm -rf .snakemake/
rm -rf logs/
......
workflow/rules/paired_end.snakefile.smk
+ 6
− 6
View file @ dc2afcf9
......@@ -11,7 +11,7 @@ rule pe_fastqc:
threads:
2
singularity:
"docker://zavolab/fastqc:0.11.8"
"docker://zavolab/fastqc:0.11.9-slim"
log:
os.path.join(config["log_dir"],"paired_end", "{sample}", "fastqc.log")
shell:
......@@ -48,7 +48,7 @@ rule pe_remove_adapters_cutadapt:
adapter_5_mate2 = lambda wildcards:
samples_table.loc[wildcards.sample, 'fq2_5p']
singularity:
"docker://zavolab/cutadapt:1.16"
"docker://zavolab/cutadapt:1.16-slim"
threads: 8
log:
os.path.join( config["log_dir"], "paired_end", "{sample}", "remove_adapters_cutadapt.log")
......@@ -99,7 +99,7 @@ rule pe_remove_polya_cutadapt:
polya_3_mate2 = lambda wildcards:
samples_table.loc[wildcards.sample, 'fq2_polya'],
singularity:
"docker://zavolab/cutadapt:1.16"
"docker://zavolab/cutadapt:1.16-slim"
threads: 8
log:
os.path.join( config["log_dir"], "paired_end", "{sample}", "remove_polya_cutadapt.log")
......@@ -176,7 +176,7 @@ rule pe_map_genome_star:
samples_table.loc[wildcards.sample, "pass_mode"]
singularity:
"docker://zavolab/star:2.6.0a"
"docker://zavolab/star:2.7.3a-slim"
threads: 12
......@@ -224,7 +224,7 @@ rule pe_index_genomic_alignment_samtools:
"map_genome",
"{sample}_Aligned.sortedByCoord.out.bam.bai"),
singularity:
"docker://zavolab/samtools:1.8"
"docker://zavolab/samtools:1.10-slim"
log:
os.path.join( config["log_dir"], "paired_end", "{sample}", "index_genomic_alignment_samtools.log")
shell:
......@@ -326,7 +326,7 @@ rule pe_genome_quantification_kallisto:
directionality = lambda wildcards:
samples_table.loc[wildcards.sample, "kallisto_directionality"]
singularity:
"docker://zavolab/kallisto:0.46.1"
"docker://zavolab/kallisto:0.46.1-slim"
threads: 8
log:
os.path.join(config["log_dir"], "paired_end", "{sample}", "genome_quantification_kallisto.log")
......
workflow/rules/single_end.snakefile.smk
+ 7
− 7
View file @ dc2afcf9
......@@ -8,7 +8,7 @@ rule fastqc:
params:
seqmode= lambda wildcards: samples_table.loc[wildcards.sample, "seqmode"]
singularity:
"docker://zavolab/fastqc:0.11.8"
"docker://zavolab/fastqc:0.11.9-slim"
log:
os.path.join(config["log_dir"], "single_end", "{sample}", "fastqc.log")
shell:
......@@ -31,7 +31,7 @@ rule remove_adapters_cutadapt:
samples_table.loc[wildcards.sample, 'fq1_5p']
singularity:
"docker://zavolab/cutadapt:1.16"
"docker://zavolab/cutadapt:1.16-slim"
threads: 8
log:
os.path.join(config["log_dir"], "single_end", "{sample}", "remove_adapters_cutadapt.log")
......@@ -58,7 +58,7 @@ rule remove_polya_cutadapt:
polya_3 = lambda wildcards:
samples_table.loc[wildcards.sample, "fq1_polya"]
singularity:
"docker://zavolab/cutadapt:1.16"
"docker://zavolab/cutadapt:1.16-slim"
threads: 8
log:
os.path.join(config["log_dir"], "single_end", "{sample}", "remove_polya_cutadapt.log")
......@@ -112,9 +112,9 @@ rule map_genome_star:
soft_clip = lambda wildcards:
samples_table.loc[wildcards.sample, "soft_clip"],
pass_mode = lambda wildcards:
samples_table.loc[wildcards.sample, "pass_mode"],
samples_table.loc[wildcards.sample, "pass_mode"],
singularity:
"docker://zavolab/star:2.6.0a"
"docker://zavolab/star:2.7.3a-slim"
threads: 12
log:
os.path.join(config["log_dir"], "single_end", "{sample}", "map_genome_star.log")
......@@ -157,7 +157,7 @@ rule index_genomic_alignment_samtools:
"map_genome",
"{sample}_Aligned.sortedByCoord.out.bam.bai")
singularity:
"docker://zavolab/samtools:1.8"
"docker://zavolab/samtools:1.10-slim"
threads: 1
log:
os.path.join(config["log_dir"], "single_end", "{sample}", "index_genomic_alignment_samtools.log")
......@@ -252,7 +252,7 @@ rule genome_quantification_kallisto:
log:
os.path.join(config["log_dir"], "single_end", "{sample}", "genome_quantification_kallisto.log.log")
singularity:
"docker://zavolab/kallisto:0.46.1"
"docker://zavolab/kallisto:0.46.1-slim"
shell:
"(kallisto quant \
-i {input.index} \
......
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