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Commit e791ce60 authored by Dominik Burri's avatar Dominik Burri
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add --no-hooks for CI tests, mark output files of salmon for multiqc, adjust files for md5 check.

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1 merge request!78Remove unnecessary files in results directory
Pipeline #11776 passed
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with 37 additions and 41 deletions
tests/test_alfa/test.sh
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− 0
View file @ e791ce60
......@@ -34,6 +34,7 @@ snakemake \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--verbose \
--notemp \
--no-hooks \
results/ALFA/ALFA_plots_mqc.png
# Check md5 sum of some output files
......
tests/test_create_dag_image/test.sh
+ 1
− 0
View file @ e791ce60
......@@ -27,5 +27,6 @@ snakemake \
--dryrun \
--verbose \
--notemp \
--no-hooks \
| dot -Tsvg > "../../images/dag_test_workflow.svg"
tests/test_create_rule_graph/test.sh
+ 1
− 0
View file @ e791ce60
......@@ -27,5 +27,6 @@ snakemake \
--dryrun \
--verbose \
--notemp \
--no-hooks \
| dot -Tsvg > "../../images/rule_graph.svg"
tests/test_integration_workflow/expected_output.md5
+ 0
− 18
View file @ e791ce60
......@@ -20,7 +20,6 @@ ea36f062eedc7f54ceffea2b635a25a8 results/star_indexes/homo_sapiens/75/STAR_inde
500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
1c0796d7e0bdab0e99780b2e11d80c19 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate2.fastq
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.SJ.out.tab
9896744dd90ff3eef00c91fa1f721366 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc_data.txt
6946ba80af318b9c1052b264dc674a51 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
2603f3031242e97411a71571f6ad9e53 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/summary.txt
......@@ -45,18 +44,9 @@ b28aac49f537b8cba364b6422458ad28 results/samples/synthetic_10_reads_paired_synt
69b70e3f561b749bf10b186dd2480a8a results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_quality.png
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
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
2e77276535976efccb244627231624bf results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv
d013650f813b815a790c9e6a51c7559b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam
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
981b59830d74d300bb5dd3e602e0d86f results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/lib_format_counts.json
989d6ee63b728fced9ec0249735ab83d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/ambig_info.tsv
3407f87245d0003e0ffbfdf6d8c04f20 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/expected_bias
92bcd0592d22a6a58d0360fc76103e56 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias
92bcd0592d22a6a58d0360fc76103e56 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias_3p
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/unmapped_names.txt
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
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.SJ.out.tab
fdb8c6ddd39b606414b2785d6ec2da8a 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_data.txt
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
fc276a1711cc35f7a9d5328bdbbab810 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/summary.txt
......@@ -69,15 +59,7 @@ e4c1a39967ec9547a2e4c71c97982ee0 results/samples/synthetic_10_reads_mate_1_synt
69b70e3f561b749bf10b186dd2480a8a 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/Images/per_sequence_quality.png
b28aac49f537b8cba364b6422458ad28 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/Images/per_tile_quality.png
5b950b5dfe3c7407e9aac153db330a38 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/Images/sequence_length_distribution.png
50a9b89a9f1da2c438cb0041b64faa0e results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/abundance.tsv
fd8242418230a4edb33350be2e4f1d78 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/pseudoalignments.bam
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
d6ae863b39ca6ec5d0f63c03036f9dda results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/lib_format_counts.json
989d6ee63b728fced9ec0249735ab83d results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/ambig_info.tsv
3407f87245d0003e0ffbfdf6d8c04f20 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/expected_bias
92bcd0592d22a6a58d0360fc76103e56 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias
92bcd0592d22a6a58d0360fc76103e56 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias_3p
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/unmapped_names.txt
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
......
tests/test_integration_workflow/test.local.sh
+ 1
− 3
View file @ e791ce60
......@@ -7,9 +7,6 @@ cleanup () {
rm -rf .config/
rm -rf .fontconfig/
rm -rf .java/
rm -rf .snakemake/
rm -rf logs/
rm -rf results/
rm -rf snakemake_report.html
cd $user_dir
echo "Exit status: $rc"
......@@ -34,6 +31,7 @@ snakemake \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--notemp \
--no-hooks \
--verbose
# Create a Snakemake report after the workflow execution
......
tests/test_integration_workflow/test.slurm.sh
+ 1
− 0
View file @ e791ce60
......@@ -36,6 +36,7 @@ snakemake \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--notemp \
--no-hooks \
--verbose
# Create a Snakemake report after the workflow execution
......
tests/test_integration_workflow_multiple_lanes/expected_output.md5
+ 0
− 18
View file @ e791ce60
......@@ -20,7 +20,6 @@ ea36f062eedc7f54ceffea2b635a25a8 results/star_indexes/homo_sapiens/75/STAR_inde
500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate1.fastq
e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_adapters_mate2.fastq
1c0796d7e0bdab0e99780b2e11d80c19 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.remove_polya_mate2.fastq
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.SJ.out.tab
9896744dd90ff3eef00c91fa1f721366 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc_data.txt
6946ba80af318b9c1052b264dc674a51 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/fastqc.fo
2603f3031242e97411a71571f6ad9e53 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq1/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1_fastqc/summary.txt
......@@ -45,18 +44,9 @@ b28aac49f537b8cba364b6422458ad28 results/samples/synthetic_10_reads_paired_synt
69b70e3f561b749bf10b186dd2480a8a results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc/fq2/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2_fastqc/Images/per_sequence_quality.png
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
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
2e77276535976efccb244627231624bf results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/abundance.tsv
d013650f813b815a790c9e6a51c7559b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/quant_kallisto/pseudoalignments.bam
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
981b59830d74d300bb5dd3e602e0d86f results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/lib_format_counts.json
989d6ee63b728fced9ec0249735ab83d results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/ambig_info.tsv
3407f87245d0003e0ffbfdf6d8c04f20 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/expected_bias
92bcd0592d22a6a58d0360fc76103e56 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias
92bcd0592d22a6a58d0360fc76103e56 results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/observed_bias_3p
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/aux_info/unmapped_names.txt
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
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.SJ.out.tab
fdb8c6ddd39b606414b2785d6ec2da8a 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_data.txt
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
fc276a1711cc35f7a9d5328bdbbab810 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/summary.txt
......@@ -69,15 +59,7 @@ e4c1a39967ec9547a2e4c71c97982ee0 results/samples/synthetic_10_reads_mate_1_synt
69b70e3f561b749bf10b186dd2480a8a 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/Images/per_sequence_quality.png
b28aac49f537b8cba364b6422458ad28 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/Images/per_tile_quality.png
5b950b5dfe3c7407e9aac153db330a38 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/Images/sequence_length_distribution.png
50a9b89a9f1da2c438cb0041b64faa0e results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/abundance.tsv
fd8242418230a4edb33350be2e4f1d78 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/quant_kallisto/pseudoalignments.bam
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
d6ae863b39ca6ec5d0f63c03036f9dda results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/lib_format_counts.json
989d6ee63b728fced9ec0249735ab83d results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/ambig_info.tsv
3407f87245d0003e0ffbfdf6d8c04f20 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/expected_bias
92bcd0592d22a6a58d0360fc76103e56 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias
92bcd0592d22a6a58d0360fc76103e56 results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/observed_bias_3p
d41d8cd98f00b204e9800998ecf8427e results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/aux_info/unmapped_names.txt
3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
......
tests/test_integration_workflow_multiple_lanes/test.local.sh
+ 1
− 0
View file @ e791ce60
......@@ -34,6 +34,7 @@ snakemake \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--notemp \
--no-hooks \
--verbose
# Create a Snakemake report after the workflow execution
......
tests/test_integration_workflow_multiple_lanes/test.slurm.sh
+ 1
− 0
View file @ e791ce60
......@@ -36,6 +36,7 @@ snakemake \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files,${PWD}/../../images" \
--notemp \
--no-hooks \
--verbose
# Create a Snakemake report after the workflow execution
......
workflow/rules/paired_end.snakefile.smk
+ 15
− 1
View file @ e791ce60
......@@ -323,7 +323,21 @@ rule pe_quantification_salmon:
"samples",
"{sample}",
"{sample}.salmon.pe",
"quant.sf")
"quant.sf"),
meta_info = os.path.join(
config["output_dir"],
"samples",
"{sample}",
"{sample}.salmon.pe",
"aux_info",
"meta_info.json"),
flenDist = os.path.join(
config["output_dir"],
"samples",
"{sample}",
"{sample}.salmon.pe",
"libParams",
"flenDist.txt")
shadow: "full"
......
workflow/rules/single_end.snakefile.smk
+ 15
− 1
View file @ e791ce60
......@@ -260,7 +260,21 @@ rule quantification_salmon:
"samples",
"{sample}",
"{sample}.salmon.se",
"quant.sf")
"quant.sf"),
meta_info = os.path.join(
config["output_dir"],
"samples",
"{sample}",
"{sample}.salmon.se",
"aux_info",
"meta_info.json"),
flenDist = os.path.join(
config["output_dir"],
"samples",
"{sample}",
"{sample}.salmon.se",
"libParams",
"flenDist.txt")
shadow: "full"
......
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