From ac953471b475b9f1b81ac08679d01fc4c2f98d9d Mon Sep 17 00:00:00 2001 From: Maria Katsantoni <31883096+mkatsanto@users.noreply.github.com> Date: Wed, 21 Feb 2024 11:11:14 +0100 Subject: [PATCH] feat: multiorganism support (#172) --- .../expected_output.files | 260 +++++----- .../expected_output.md5 | 224 ++++---- .../expected_output_temp_flag.files | 228 ++++----- .../expected_output_temp_flag.md5 | 180 +++---- tests/test_integration_workflow/test.local.sh | 18 +- tests/test_integration_workflow/test.slurm.sh | 16 +- .../test.temp.flag.sh | 12 +- .../expected_output.md5 | 224 ++++---- .../test.local.sh | 12 +- .../test.slurm.sh | 12 +- .../expected_output.files | 260 +++++----- .../expected_output.md5 | 224 ++++---- .../test.local.sh | 12 +- .../test.slurm.sh | 12 +- workflow/Snakefile | 477 +++++++++++++----- workflow/rules/common.smk | 6 + workflow/rules/paired_end.snakefile.smk | 82 ++- workflow/rules/single_end.snakefile.smk | 75 ++- 18 files changed, 1340 insertions(+), 994 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results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq1_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya_fastqc/Images/sequence_length_distribution.png +1a637a2f5ad12b4d09902683c248e25b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/fastqc_data.txt +8703b1221f93cbf3f33fdd8fe09a7445 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/fastqc.fo +bbc122792bc83635263ee7f6e581e0af results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/summary.txt +8bdd1dfd781d3b35790798718b1fb69c results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/adapter_content.png +3bea9709a7970bd7244e2fa633f4ad65 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/duplication_levels.png +153a562878843918e1f49e892cbffd86 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_base_n_content.png +fb393c8344df3e64b354ac5d4943c3c4 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_base_quality.png +2a0822e0d2a8033a70ce33b291fb1567 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_base_sequence_content.png +df6571951d97a245811459f813e871f0 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_gc_content.png +dcf48859481e37d33dbe4ceac1764af9 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_quality.png +f399fa5792cdfb72fac7ae2226723122 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_tile_quality.png +3a7a9fdec464c6059f5175a3d610a345 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/sequence_length_distribution.png diff --git a/tests/test_integration_workflow/test.local.sh b/tests/test_integration_workflow/test.local.sh index 347c03e..ad9a20b 100755 --- a/tests/test_integration_workflow/test.local.sh +++ b/tests/test_integration_workflow/test.local.sh @@ -38,16 +38,16 @@ snakemake \ --report="snakemake_report.html" # Check md5 sum of some output files -find results/ -type f -name \*\.gz -exec gunzip '{}' \; -find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; +find results/homo_sapiens/ -type f -name \*\.gz -exec gunzip '{}' \; +find results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; md5sum --check "expected_output.md5" # Checksum file generated with -#find results/ \ +#find results/homo_sapiens/ \ # -type f \ # -name \*\.gz \ # -exec gunzip '{}' \; -#find results/ \ +#find results/homo_sapiens/ \ # -type f \ # -name \*\.zip \ # -exec sh -c 'unzip -o {} -d $(dirname {})' \; @@ -60,7 +60,7 @@ md5sum --check "expected_output.md5" echo "Verifying STAR output" result=$(bedtools intersect -F 1 -v -bed \ -a ../input_files/synthetic.mate_1.bed \ - -b 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.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -68,7 +68,7 @@ if [ $result != "0" ]; then fi result=$(bedtools intersect -F 1 -v -bed \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ - -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -78,8 +78,8 @@ fi # Check whether Salmon assigns reads to expected genes echo "Verifying Salmon output" diff \ - <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff \ - <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ - <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') + <(cat results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') \ No newline at end of file diff --git a/tests/test_integration_workflow/test.slurm.sh b/tests/test_integration_workflow/test.slurm.sh index 889d078..32a0bc6 100755 --- a/tests/test_integration_workflow/test.slurm.sh +++ b/tests/test_integration_workflow/test.slurm.sh @@ -38,16 +38,16 @@ snakemake \ --report="snakemake_report.html" # Check md5 sum of some output files -find results/ -type f -name \*\.gz -exec gunzip '{}' \; -find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; +find results/homo_sapiens/ -type f -name \*\.gz -exec gunzip '{}' \; +find results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; md5sum --check "expected_output.md5" # Checksum file generated with -# find results/ \ +# find results/homo_sapiens/ \ # -type f \ # -name \*\.gz \ # -exec gunzip '{}' \; -# find results/ \ +# find results/homo_sapiens/ \ # -type f \ # -name \*\.zip \ # -exec sh -c 'unzip -o {} -d $(dirname {})' \; @@ -60,7 +60,7 @@ md5sum --check "expected_output.md5" echo "Verifying STAR output" result=$(bedtools intersect -F 1 -v -bed \ -a ../input_files/synthetic.mate_1.bed \ - -b 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.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -68,7 +68,7 @@ if [ $result != "0" ]; then fi result=$(bedtools intersect -F 1 -v -bed \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ - -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -78,8 +78,8 @@ fi # Check whether Salmon assigns reads to expected genes echo "Verifying Salmon output" diff \ - <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff \ - <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff --git a/tests/test_integration_workflow/test.temp.flag.sh b/tests/test_integration_workflow/test.temp.flag.sh index 2ef0766..b169259 100755 --- a/tests/test_integration_workflow/test.temp.flag.sh +++ b/tests/test_integration_workflow/test.temp.flag.sh @@ -37,8 +37,8 @@ snakemake \ --report="snakemake_report.html" # Check md5 sum of some output files -find results/ -type f -name \*\.gz -exec gunzip '{}' \; -find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; +find results/homo_sapiens/ -type f -name \*\.gz -exec gunzip '{}' \; +find results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; md5sum --check "expected_output_temp_flag.md5" # Check whether STAR produces expected alignments @@ -48,7 +48,7 @@ md5sum --check "expected_output_temp_flag.md5" echo "Verifying STAR output" result=$(bedtools intersect -F 1 -v -bed \ -a ../input_files/synthetic.mate_1.bed \ - -b 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.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -56,7 +56,7 @@ if [ $result != "0" ]; then fi result=$(bedtools intersect -F 1 -v -bed \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ - -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -66,9 +66,9 @@ fi # Check whether Salmon assigns reads to expected genes echo "Verifying Salmon output" diff \ - <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff \ - <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff --git a/tests/test_integration_workflow_multiple_lanes/expected_output.md5 b/tests/test_integration_workflow_multiple_lanes/expected_output.md5 index d7749ca..fa57220 100644 --- a/tests/test_integration_workflow_multiple_lanes/expected_output.md5 +++ b/tests/test_integration_workflow_multiple_lanes/expected_output.md5 @@ -16,118 +16,118 @@ bae93882f9148a6c55816b733c32a3a2 results/star_indexes/homo_sapiens/75/STAR_inde 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 65e794aa5096551254af18a678d02264 results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab -500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_adapters.fastq -500dd49da40b16799aba62aa5cf239ba results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya.fastq -e90e31db1ce51d930645eb74ff70d21b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_adapters.fastq -1c0796d7e0bdab0e99780b2e11d80c19 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results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_base_sequence_content.png +df6571951d97a245811459f813e871f0 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_gc_content.png +dcf48859481e37d33dbe4ceac1764af9 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_quality.png +f399fa5792cdfb72fac7ae2226723122 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_tile_quality.png +3a7a9fdec464c6059f5175a3d610a345 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/sequence_length_distribution.png diff --git a/tests/test_integration_workflow_multiple_lanes/test.local.sh b/tests/test_integration_workflow_multiple_lanes/test.local.sh index d2499cf..5884517 100755 --- a/tests/test_integration_workflow_multiple_lanes/test.local.sh +++ b/tests/test_integration_workflow_multiple_lanes/test.local.sh @@ -38,8 +38,8 @@ snakemake \ --report="snakemake_report.html" # Check md5 sum of some output files -find results/ -type f -name \*\.gz -exec gunzip '{}' \; -find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; +find results/homo_sapiens/ -type f -name \*\.gz -exec gunzip '{}' \; +find results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; md5sum --check "expected_output.md5" # Check whether STAR produces expected alignments @@ -49,7 +49,7 @@ md5sum --check "expected_output.md5" echo "Verifying STAR output" result=$(bedtools intersect -F 1 -v -bed \ -a ../input_files/synthetic.mate_1.bed \ - -b 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.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -57,7 +57,7 @@ if [ $result != "0" ]; then fi result=$(bedtools intersect -F 1 -v -bed \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ - -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -67,8 +67,8 @@ fi # Check whether Salmon assigns reads to expected genes echo "Verifying Salmon output" diff \ - <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff \ - <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff --git a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh index cf57636..9a26722 100755 --- a/tests/test_integration_workflow_multiple_lanes/test.slurm.sh +++ b/tests/test_integration_workflow_multiple_lanes/test.slurm.sh @@ -38,8 +38,8 @@ snakemake \ --report="snakemake_report.html" # Check md5 sum of some output files -find results/ -type f -name \*\.gz -exec gunzip '{}' \; -find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; +find results/homo_sapiens/ -type f -name \*\.gz -exec gunzip '{}' \; +find results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; md5sum --check "expected_output.md5" # Check whether STAR produces expected alignments @@ -49,7 +49,7 @@ md5sum --check "expected_output.md5" echo "Verifying STAR output" result=$(bedtools intersect -F 1 -v -bed \ -a ../input_files/synthetic.mate_1.bed \ - -b 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.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -57,7 +57,7 @@ if [ $result != "0" ]; then fi result=$(bedtools intersect -F 1 -v -bed \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ - -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -67,8 +67,8 @@ fi # Check whether Salmon assigns reads to expected genes echo "Verifying Salmon output" diff \ - <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff \ - <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff --git a/tests/test_integration_workflow_with_conda/expected_output.files b/tests/test_integration_workflow_with_conda/expected_output.files index 78afce0..b27f77b 100644 --- a/tests/test_integration_workflow_with_conda/expected_output.files +++ b/tests/test_integration_workflow_with_conda/expected_output.files @@ -16,136 +16,136 @@ results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_adapters.fastq -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya.fastq -results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_adapters.fastq 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results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq1_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya_fastqc/Images/per_base_quality.png +44f6e7049ccba41451b593f34200d694 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq1_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya_fastqc/Images/per_base_sequence_content.png +272768226634a55c14bd9355faacc49c results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq1_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya_fastqc/Images/per_sequence_gc_content.png +d27d5858f5517ee659c15363a37a3b8d results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq1_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya_fastqc/Images/per_sequence_quality.png +f399fa5792cdfb72fac7ae2226723122 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq1_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya_fastqc/Images/per_tile_quality.png +c344a6439fadffbc4a73f8ba1f4050d2 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq1_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya_fastqc/Images/sequence_length_distribution.png +1a637a2f5ad12b4d09902683c248e25b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/fastqc_data.txt +8703b1221f93cbf3f33fdd8fe09a7445 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/fastqc.fo +bbc122792bc83635263ee7f6e581e0af results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/summary.txt +d32ef2a883c08844ae386db8f39b3754 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/adapter_content.png +c3fb12780b1c389d7e2b67c5387865c0 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/duplication_levels.png +615e8ed0536132667a931933db4c11d9 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_base_n_content.png +fb393c8344df3e64b354ac5d4943c3c4 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_base_quality.png +793ce54855a9765c722efe0b02221c3c results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_base_sequence_content.png +2a12a72a2e561b61d2629ddee40e7ca4 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_gc_content.png +c1c267daf0b12f68d9b565a7deb123cf results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_sequence_quality.png +f399fa5792cdfb72fac7ae2226723122 results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/per_tile_quality.png +3ebe15878142b0967f366956e5e6120d results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/sequence_length_distribution.png diff --git a/tests/test_integration_workflow_with_conda/test.local.sh b/tests/test_integration_workflow_with_conda/test.local.sh index 3e57cfc..778a49f 100755 --- a/tests/test_integration_workflow_with_conda/test.local.sh +++ b/tests/test_integration_workflow_with_conda/test.local.sh @@ -38,8 +38,8 @@ snakemake \ --report="snakemake_report.html" # Check md5 sum of some output files -find results/ -type f -name \*\.gz -exec gunzip '{}' \; -find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; +find results/homo_sapiens/ -type f -name \*\.gz -exec gunzip '{}' \; +find results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; md5sum --check "expected_output.md5" # Check whether STAR produces expected alignments @@ -49,7 +49,7 @@ md5sum --check "expected_output.md5" echo "Verifying STAR output" result=$(bedtools intersect -F 1 -v -bed \ -a ../input_files/synthetic.mate_1.bed \ - -b 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.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -57,7 +57,7 @@ if [ $result != "0" ]; then fi result=$(bedtools intersect -F 1 -v -bed \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ - -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -67,8 +67,8 @@ fi # Check whether Salmon assigns reads to expected genes echo "Verifying Salmon output" diff \ - <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff \ - <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff --git a/tests/test_integration_workflow_with_conda/test.slurm.sh b/tests/test_integration_workflow_with_conda/test.slurm.sh index 1c5616e..9b72556 100755 --- a/tests/test_integration_workflow_with_conda/test.slurm.sh +++ b/tests/test_integration_workflow_with_conda/test.slurm.sh @@ -38,8 +38,8 @@ snakemake \ --report="snakemake_report.html" # Check md5 sum of some output files -find results/ -type f -name \*\.gz -exec gunzip '{}' \; -find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; +find results/homo_sapiens/ -type f -name \*\.gz -exec gunzip '{}' \; +find results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; md5sum --check "expected_output.md5" # Check whether STAR produces expected alignments @@ -49,7 +49,7 @@ md5sum --check "expected_output.md5" echo "Verifying STAR output" result=$(bedtools intersect -F 1 -v -bed \ -a ../input_files/synthetic.mate_1.bed \ - -b 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.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/map_genome/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.se.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -57,7 +57,7 @@ if [ $result != "0" ]; then fi result=$(bedtools intersect -F 1 -v -bed \ -a <(cat ../input_files/synthetic.mate_1.bed ../input_files/synthetic.mate_2.bed) \ - -b results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ + -b results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/map_genome/synthetic_10_reads_paired_synthetic_10_reads_paired.pe.Aligned.sortedByCoord.out.bam \ | wc -l) if [ $result != "0" ]; then echo "Alignments for mate 1 reads are not consistent with ground truth" @@ -67,8 +67,8 @@ fi # Check whether Salmon assigns reads to expected genes echo "Verifying Salmon output" diff \ - <(cat results/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.salmon.se/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff \ - <(cat results/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ + <(cat results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.salmon.pe/quant.genes.sf | cut -f1,5 | tail -n +2 | sort -k1,1) \ <(cat ../input_files/synthetic.mate_1.bed | cut -f7 | sort | uniq -c | sort -k2nr | awk '{printf($2"\t"$1"\n")}') diff --git a/workflow/Snakefile b/workflow/Snakefile index fda39fe..0a3648b 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -132,43 +132,67 @@ rule finish: Rule for collecting outputs """ input: - multiqc_report=os.path.join(config["output_dir"], "multiqc_summary"), + multiqc_report=expand( + os.path.join(config["output_dir"], "{organism}", "multiqc_summary"), + organism=pd.unique(samples_table["organism"].values), + ), bigWig=expand( - os.path.join( - config["output_dir"], - "samples", - "{sample}", - "bigWig", - "{renamed_unique}", - "{sample}_{renamed_unique}_{strand}.bw", + expand( + os.path.join( + config["output_dir"], + "{organism}", + "samples", + "{sample}", + "bigWig", + "{{renamed_unique}}", + "{sample}_{{renamed_unique}}_{{strand}}.bw", + ), + zip, + sample=pd.unique(samples_table.index.values), + organism=[ + get_sample("organism", search_id="index", search_value=j) + for j in pd.unique(samples_table.index.values) + ], ), - sample=pd.unique(samples_table.index.values), strand=["plus", "minus"], renamed_unique=alfa_dict.keys(), ), salmon_merge_genes=expand( os.path.join( config["output_dir"], + "{organism}", "summary_salmon", "quantmerge", "genes_{salmon_merge_on}.tsv", ), + organism=pd.unique(samples_table["organism"].values), salmon_merge_on=["tpm", "numreads"], ), salmon_merge_transcripts=expand( os.path.join( config["output_dir"], + "{organism}", "summary_salmon", "quantmerge", "transcripts_{salmon_merge_on}.tsv", ), + organism=pd.unique(samples_table["organism"].values), salmon_merge_on=["tpm", "numreads"], ), - kallisto_merge_transcripts=os.path.join( - config["output_dir"], "summary_kallisto", "transcripts_tpm.tsv" + kallisto_merge_transcripts=expand( + os.path.join( + config["output_dir"], + "{organism}", + "summary_kallisto", + "transcripts_tpm.tsv", + ), + organism=pd.unique(samples_table["organism"].values), ), - kallisto_merge_genes=os.path.join( - config["output_dir"], "summary_kallisto", "genes_tpm.tsv" + kallisto_merge_genes=expand( + os.path.join( + config["output_dir"], "{organism}", "summary_kallisto", "genes_tpm.tsv" + ), + organism=pd.unique(samples_table["organism"].values), ), @@ -186,6 +210,7 @@ rule start: output: reads=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "start", @@ -196,12 +221,14 @@ rule start: log: stderr=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{sample}}.{{mate}}.stderr.log", ), stdout=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{sample}}.{{mate}}.stdout.log", @@ -223,6 +250,7 @@ rule fastqc: input: reads=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "start", @@ -231,7 +259,12 @@ rule fastqc: output: outdir=directory( os.path.join( - config["output_dir"], "samples", "{sample}", "fastqc", "{mate}" + config["output_dir"], + "{organism}", + "samples", + "{sample}", + "fastqc", + "{mate}", ) ), params: @@ -249,12 +282,14 @@ rule fastqc: log: stderr=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{mate}}.stderr.log", ), stdout=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{mate}}.stdout.log", @@ -278,6 +313,7 @@ rule fastqc_trimmed: input: reads=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.{mate}.{seqmode}.remove_polya.fastq.gz", @@ -286,6 +322,7 @@ rule fastqc_trimmed: outdir=directory( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "fastqc_trimmed", @@ -305,12 +342,14 @@ rule fastqc_trimmed: log: stderr=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{seqmode}}_{{mate}}.stderr.log", ), stdout=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{seqmode}}_{{mate}}.stdout.log", @@ -381,10 +420,14 @@ rule create_index_star: mem_mb=lambda wildcards, attempt: 32000 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}_{{index_size}}.stderr.log" + config["log_dir"], + "{organism}", + f"{current_rule}_{{index_size}}.stderr.log", ), stdout=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}_{{index_size}}.stdout.log" + config["log_dir"], + "{organism}", + f"{current_rule}_{{index_size}}.stdout.log", ), shell: "(mkdir -p {params.output_dir}; \ @@ -427,10 +470,10 @@ rule sort_gtf: mem_mb=lambda wildcards, attempt: 32000 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}.stderr.log" + config["log_dir"], "{organism}", f"{current_rule}.stderr.log" ), stdout=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}.stdout.log" + config["log_dir"], "{organism}", f"{current_rule}.stdout.log" ), shell: "(sort \ @@ -477,8 +520,8 @@ rule extract_transcriptome: resources: mem_mb=lambda wildcards, attempt: 4096 * attempt, log: - stderr=os.path.join(config["log_dir"], f"{current_rule}_{{organism}}.log"), - stdout=os.path.join(config["log_dir"], f"{current_rule}_{{organism}}.log"), + stderr=os.path.join(config["log_dir"], "{organism}", f"{current_rule}.log"), + stdout=os.path.join(config["log_dir"], "{organism}", f"{current_rule}.log"), shell: "(gffread \ -w {output.transcriptome} \ @@ -519,7 +562,7 @@ rule concatenate_transcriptome_and_genome: mem_mb=lambda wildcards, attempt: 4096 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}.stderr.log" + config["log_dir"], "{organism}", f"{current_rule}.stderr.log" ), shell: "(cat {input.transcriptome} {input.genome} \ @@ -543,7 +586,7 @@ rule create_index_salmon: ), chr_names=lambda wildcards: os.path.join( config["star_indexes"], - get_sample("organism"), + "{organism}", get_sample("index_size"), "STAR_index", "chrName.txt", @@ -576,10 +619,10 @@ rule create_index_salmon: mem_mb=lambda wildcards, attempt: 32000 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}_{{kmer}}.stderr.log" + config["log_dir"], "{organism}", f"{current_rule}_{{kmer}}.stderr.log" ), stdout=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}_{{kmer}}.stdout.log" + config["log_dir"], "{organism}", f"{current_rule}_{{kmer}}.stdout.log" ), shell: "(salmon index \ @@ -619,10 +662,10 @@ rule create_index_kallisto: mem_mb=lambda wildcards, attempt: 8192 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}.stderr.log" + config["log_dir"], "{organism}", f"{current_rule}_.stderr.log" ), stdout=os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}.stdout.log" + config["log_dir"], "{organism}", f"{current_rule}_.stdout.log" ), shell: "(mkdir -p {params.output_dir}; \ @@ -644,12 +687,16 @@ rule extract_transcripts_as_bed12: input: gtf=lambda wildcards: os.path.join( config["star_indexes"], - get_sample("organism"), + wildcards.organism, "sorted_genome.gtf", ), output: bed12=temp( - os.path.join(config["output_dir"], "full_transcripts_protein_coding.bed") + os.path.join( + config["output_dir"], + "{organism}", + "full_transcripts_protein_coding.bed", + ) ), params: cluster_log_path=config["cluster_log_dir"], @@ -669,8 +716,12 @@ rule extract_transcripts_as_bed12: resources: mem_mb=lambda wildcards, attempt: 4096 * attempt, log: - stdout=os.path.join(config["log_dir"], f"{current_rule}.stdout.log"), - stderr=os.path.join(config["log_dir"], f"{current_rule}.stderr.log"), + stdout=os.path.join( + config["log_dir"], "{organism}", f"{current_rule}.stdout.log" + ), + stderr=os.path.join( + config["log_dir"], "{organism}", f"{current_rule}.stderr.log" + ), shell: "(gtf2bed12 \ --gtf {input.gtf} \ @@ -689,6 +740,7 @@ rule sort_genomic_alignment_samtools: input: bam=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", @@ -697,6 +749,7 @@ rule sort_genomic_alignment_samtools: output: bam=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", @@ -717,12 +770,14 @@ rule sort_genomic_alignment_samtools: log: stderr=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}.{{seqmode}}.stderr.log", ), stdout=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}.{{seqmode}}.stdout.log", @@ -746,6 +801,7 @@ rule index_genomic_alignment_samtools: input: bam=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", @@ -754,6 +810,7 @@ rule index_genomic_alignment_samtools: output: bai=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", @@ -774,12 +831,14 @@ rule index_genomic_alignment_samtools: log: stderr=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}.{{seqmode}}.stderr.log", ), stdout=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}.{{seqmode}}.stdout.log", @@ -802,11 +861,15 @@ rule calculate_TIN_scores: bam=lambda wildcards: expand( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam", ), + organism=get_sample( + "organism", search_id="index", search_value=wildcards.sample + ), sample=wildcards.sample, seqmode=get_sample( "seqmode", search_id="index", search_value=wildcards.sample @@ -815,23 +878,32 @@ rule calculate_TIN_scores: bai=lambda wildcards: expand( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", "{sample}.{seqmode}.Aligned.sortedByCoord.out.bam.bai", ), + organism=get_sample( + "organism", search_id="index", search_value=wildcards.sample + ), sample=wildcards.sample, seqmode=get_sample( "seqmode", search_id="index", search_value=wildcards.sample ), ), transcripts_bed12=os.path.join( - config["output_dir"], "full_transcripts_protein_coding.bed" + config["output_dir"], "{organism}", "full_transcripts_protein_coding.bed" ), output: TIN_score=temp( os.path.join( - config["output_dir"], "samples", "{sample}", "TIN", "TIN_score.tsv" + config["output_dir"], + "{organism}", + "samples", + "{sample}", + "TIN", + "TIN_score.tsv", ) ), params: @@ -855,7 +927,11 @@ rule calculate_TIN_scores: mem_mb=lambda wildcards, attempt, input: len(input.bam) * 1024 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", f"{current_rule}.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + f"{current_rule}.log", ), shell: "(calculate-tin.py \ @@ -875,46 +951,57 @@ rule salmon_quantmerge_genes: Merge gene quantifications into a single file """ input: - salmon_in=expand( + salmon_in=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "{sample}.salmon.{seqmode}", "quant.sf", ), zip, - sample=pd.unique(samples_table.index.values), + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), seqmode=[ get_sample("seqmode", search_id="index", search_value=i) - for i in pd.unique(samples_table.index.values) + for i in get_all_samples( + search_id="organism", search_value=wildcards.organism + ) ], ), output: salmon_out=os.path.join( config["output_dir"], + "{organism}", "summary_salmon", "quantmerge", "genes_{salmon_merge_on}.tsv", ), params: cluster_log_path=config["cluster_log_dir"], - salmon_in=expand( + salmon_in=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "{sample}.salmon.{seqmode}", ), zip, - sample=[i for i in pd.unique(samples_table.index.values)], + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), seqmode=[ get_sample("seqmode", search_id="index", search_value=i) - for i in pd.unique(samples_table.index.values) + for i in get_all_samples( + search_id="organism", search_value=wildcards.organism + ) ], ), - sample_name_list=expand( - "{sample}", sample=pd.unique(samples_table.index.values) + sample_name_list=lambda wildcards: get_all_samples( + search_id="organism", search_value=wildcards.organism ), salmon_merge_on="{salmon_merge_on}", additional_params=parse_rule_config( @@ -938,10 +1025,14 @@ rule salmon_quantmerge_genes: mem_mb=lambda wildcards, attempt, input: len(input.salmon_in) * 1024 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{salmon_merge_on}}.stderr.log" + config["log_dir"], + "{organism}", + f"{current_rule}_{{salmon_merge_on}}.stderr.log", ), stdout=os.path.join( - config["log_dir"], f"{current_rule}_{{salmon_merge_on}}.stdout.log" + config["log_dir"], + "{organism}", + f"{current_rule}_{{salmon_merge_on}}.stdout.log", ), shell: "(salmon quantmerge \ @@ -962,46 +1053,60 @@ rule salmon_quantmerge_transcripts: Merge transcript quantifications into a single file """ input: - salmon_in=expand( + salmon_in=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "{sample}.salmon.{seqmode}", "quant.sf", ), zip, - sample=[i for i in pd.unique(samples_table.index.values)], + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), seqmode=[ get_sample("seqmode", search_id="index", search_value=i) - for i in pd.unique(samples_table.index.values) + for i in get_all_samples( + search_id="organism", search_value=wildcards.organism + ) ], ), output: salmon_out=os.path.join( config["output_dir"], + "{organism}", "summary_salmon", "quantmerge", "transcripts_{salmon_merge_on}.tsv", ), params: cluster_log_path=config["cluster_log_dir"], - salmon_in=expand( + salmon_in=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "{sample}.salmon.{seqmode}", ), zip, - sample=[i for i in pd.unique(samples_table.index.values)], + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), seqmode=[ get_sample("seqmode", search_id="index", search_value=i) - for i in pd.unique(samples_table.index.values) + for i in get_all_samples( + search_id="organism", search_value=wildcards.organism + ) ], ), - sample_name_list=expand( - "{sample}", sample=pd.unique(samples_table.index.values) + sample_name_list=lambda wildcards: expand( + "{sample}", + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), ), salmon_merge_on="{salmon_merge_on}", additional_params=parse_rule_config( @@ -1025,10 +1130,14 @@ rule salmon_quantmerge_transcripts: mem_mb=lambda wildcards, attempt, input: len(input.salmon_in) * 1000 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{salmon_merge_on}}.stderr.log" + config["log_dir"], + "{organism}", + f"{current_rule}_{{salmon_merge_on}}.stderr.log", ), stdout=os.path.join( - config["log_dir"], f"{current_rule}_{{salmon_merge_on}}.stdout.log" + config["log_dir"], + "{organism}", + f"{current_rule}_{{salmon_merge_on}}.stdout.log", ), shell: "(salmon quantmerge \ @@ -1048,48 +1157,58 @@ rule kallisto_merge_genes: Merge gene quantifications into single file """ input: - pseudoalignment=expand( + pseudoalignment=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "quant_kallisto", "{sample}.{seqmode}.kallisto.pseudo.sam", ), zip, - sample=[i for i in pd.unique(samples_table.index.values)], + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), seqmode=[ get_sample("seqmode", search_id="index", search_value=i) - for i in pd.unique(samples_table.index.values) + for i in get_all_samples( + search_id="organism", search_value=wildcards.organism + ) ], ), gtf=lambda wildcards: os.path.join( config["star_indexes"], - get_sample("organism"), + wildcards.organism, "sorted_genome.gtf", ), output: - gn_tpm=os.path.join(config["output_dir"], "summary_kallisto", "genes_tpm.tsv"), + gn_tpm=os.path.join( + config["output_dir"], "{organism}", "summary_kallisto", "genes_tpm.tsv" + ), gn_counts=os.path.join( - config["output_dir"], "summary_kallisto", "genes_counts.tsv" + config["output_dir"], "{organism}", "summary_kallisto", "genes_counts.tsv" ), params: cluster_log_path=config["cluster_log_dir"], dir_out=lambda wildcards, output: os.path.dirname(output.gn_counts), - tables=",".join( + tables=lambda wildcards: ",".join( expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "quant_kallisto", "abundance.h5", ), - sample=[i for i in pd.unique(samples_table.index.values)], + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), ) ), - sample_name_list=",".join( - expand("{sample}", sample=pd.unique(samples_table.index.values)) + sample_name_list=lambda wildcards: ",".join( + get_all_samples(search_id="organism", search_value=wildcards.organism), ), additional_params=parse_rule_config( rule_config, @@ -1112,8 +1231,12 @@ rule kallisto_merge_genes: * 1000 * attempt, log: - stderr=os.path.join(config["log_dir"], f"{current_rule}.stderr.log"), - stdout=os.path.join(config["log_dir"], f"{current_rule}.stdout.log"), + stderr=os.path.join( + config["log_dir"], "{organism}", f"{current_rule}.stderr.log" + ), + stdout=os.path.join( + config["log_dir"], "{organism}", f"{current_rule}.stdout.log" + ), shell: "(merge_kallisto.R \ --input {params.tables} \ @@ -1133,45 +1256,59 @@ rule kallisto_merge_transcripts: Merge transcript quantifications into a single files """ input: - pseudoalignment=expand( + pseudoalignment=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "quant_kallisto", "{sample}.{seqmode}.kallisto.pseudo.sam", ), zip, - sample=[i for i in pd.unique(samples_table.index.values)], + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), seqmode=[ get_sample("seqmode", search_id="index", search_value=i) - for i in pd.unique(samples_table.index.values) + for i in get_all_samples( + search_id="organism", search_value=wildcards.organism + ) ], ), output: tx_tpm=os.path.join( - config["output_dir"], "summary_kallisto", "transcripts_tpm.tsv" + config["output_dir"], + "{organism}", + "summary_kallisto", + "transcripts_tpm.tsv", ), tx_counts=os.path.join( - config["output_dir"], "summary_kallisto", "transcripts_counts.tsv" + config["output_dir"], + "{organism}", + "summary_kallisto", + "transcripts_counts.tsv", ), params: cluster_log_path=config["cluster_log_dir"], dir_out=lambda wildcards, output: os.path.dirname(output.tx_counts), - tables=",".join( + tables=lambda wildcards: ",".join( expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "quant_kallisto", "abundance.h5", ), - sample=[i for i in pd.unique(samples_table.index.values)], + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), ) ), - sample_name_list=",".join( - expand("{sample}", sample=pd.unique(samples_table.index.values)) + sample_name_list=lambda wildcards: ",".join( + get_all_samples(search_id="organism", search_value=wildcards.organism) ), additional_params=parse_rule_config( rule_config, @@ -1193,8 +1330,12 @@ rule kallisto_merge_transcripts: * 1024 * attempt, log: - stderr=os.path.join(config["log_dir"], f"{current_rule}.stderr.log"), - stdout=os.path.join(config["log_dir"], f"{current_rule}.stdout.log"), + stderr=os.path.join( + config["log_dir"], "{organism}", f"{current_rule}.stderr.log" + ), + stdout=os.path.join( + config["log_dir"], "{organism}", f"{current_rule}.stdout.log" + ), shell: "(merge_kallisto.R \ --input {params.tables} \ @@ -1210,11 +1351,17 @@ current_rule = "pca_salmon" rule pca_salmon: input: tpm=os.path.join( - config["output_dir"], "summary_salmon", "quantmerge", "{molecule}_tpm.tsv" + config["output_dir"], + "{organism}", + "summary_salmon", + "quantmerge", + "{molecule}_tpm.tsv", ), output: out=directory( - os.path.join(config["output_dir"], "zpca", "pca_salmon_{molecule}") + os.path.join( + config["output_dir"], "{organism}", "zpca", "pca_salmon_{molecule}" + ) ), params: cluster_log_path=config["cluster_log_dir"], @@ -1235,10 +1382,10 @@ rule pca_salmon: mem_mb=lambda wildcards, attempt: 4096 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{molecule}}.stderr.log" + config["log_dir"], "{organism}", f"{current_rule}_{{molecule}}.stderr.log" ), stdout=os.path.join( - config["log_dir"], f"{current_rule}_{{molecule}}.stdout.log" + config["log_dir"], "{organism}", f"{current_rule}_{{molecule}}.stdout.log" ), shell: "(zpca-tpm \ @@ -1253,10 +1400,17 @@ current_rule = "pca_kallisto" rule pca_kallisto: input: - tpm=os.path.join(config["output_dir"], "summary_kallisto", "{molecule}_tpm.tsv"), + tpm=os.path.join( + config["output_dir"], + "{organism}", + "summary_kallisto", + "{molecule}_tpm.tsv", + ), output: out=directory( - os.path.join(config["output_dir"], "zpca", "pca_kallisto_{molecule}") + os.path.join( + config["output_dir"], "{organism}", "zpca", "pca_kallisto_{molecule}" + ) ), params: cluster_log_path=config["cluster_log_dir"], @@ -1277,10 +1431,10 @@ rule pca_kallisto: mem_mb=lambda wildcards, attempt: 4096 * attempt, log: stderr=os.path.join( - config["log_dir"], f"{current_rule}_{{molecule}}.stderr.log" + config["log_dir"], "{organism}", f"{current_rule}_{{molecule}}.stderr.log" ), stdout=os.path.join( - config["log_dir"], f"{current_rule}_{{molecule}}.stdout.log" + config["log_dir"], "{organism}", f"{current_rule}_{{molecule}}.stdout.log" ), shell: "(zpca-tpm \ @@ -1301,6 +1455,7 @@ rule star_rpm: bam=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "map_genome", @@ -1314,6 +1469,7 @@ rule star_rpm: bai=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "map_genome", @@ -1328,6 +1484,7 @@ rule star_rpm: str1=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "STAR_coverage", @@ -1337,6 +1494,7 @@ rule star_rpm: str2=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "STAR_coverage", @@ -1346,6 +1504,7 @@ rule star_rpm: str3=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "STAR_coverage", @@ -1355,6 +1514,7 @@ rule star_rpm: str4=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "STAR_coverage", @@ -1388,10 +1548,18 @@ rule star_rpm: mem_mb=lambda wildcards, attempt: 8192 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", f"{current_rule}_.stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + f"{current_rule}_.stderr.log", ), stdout=os.path.join( - config["log_dir"], "samples", "{sample}", f"{current_rule}_.stdout.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + f"{current_rule}_.stdout.log", ), shell: "(mkdir -p {params.out_dir}; \ @@ -1414,6 +1582,7 @@ rule rename_star_rpm_for_alfa: plus=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "STAR_coverage", @@ -1431,6 +1600,7 @@ rule rename_star_rpm_for_alfa: minus=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "STAR_coverage", @@ -1449,6 +1619,7 @@ rule rename_star_rpm_for_alfa: plus=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "ALFA", @@ -1459,6 +1630,7 @@ rule rename_star_rpm_for_alfa: minus=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "ALFA", @@ -1473,12 +1645,14 @@ rule rename_star_rpm_for_alfa: log: stderr=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{renamed_unique}}.stderr.log", ), stdout=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{renamed_unique}}.stdout.log", @@ -1551,7 +1725,7 @@ rule generate_alfa_index: mem_mb=lambda wildcards, attempt: 4096 * attempt, log: os.path.join( - config["log_dir"], f"{current_rule}_{{organism}}_{{index_size}}.log" + config["log_dir"], "{organism}", f"{current_rule}_{{index_size}}.log" ), shell: "(mkdir -p {output.temp_dir}; \ @@ -1575,23 +1749,25 @@ rule alfa_qc: input: plus=lambda wildcards: os.path.join( config["output_dir"], + wildcards.organism, "samples", wildcards.sample, "ALFA", wildcards.renamed_unique, - f"{wildcards.sample}.{wildcards.renamed_unique}.plus.bg", + wildcards.sample + "." + wildcards.renamed_unique + ".plus.bg", ), minus=lambda wildcards: os.path.join( config["output_dir"], + wildcards.organism, "samples", wildcards.sample, "ALFA", wildcards.renamed_unique, - f"{wildcards.sample}.{wildcards.renamed_unique}.minus.bg", + wildcards.sample + "." + wildcards.renamed_unique + ".minus.bg", ), gtf=lambda wildcards: os.path.join( config["alfa_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, get_sample("index_size", search_id="index", search_value=wildcards.sample), "ALFA", "sorted_genes.stranded.ALFA_index", @@ -1600,6 +1776,7 @@ rule alfa_qc: biotypes=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "ALFA", @@ -1610,6 +1787,7 @@ rule alfa_qc: categories=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "ALFA", @@ -1619,6 +1797,7 @@ rule alfa_qc: ), table=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "ALFA", @@ -1629,6 +1808,7 @@ rule alfa_qc: directory( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "ALFA", @@ -1671,6 +1851,7 @@ rule alfa_qc: log: os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}.{{renamed_unique}}.log", @@ -1744,43 +1925,64 @@ rule multiqc_report: Create report with MultiQC """ input: - fastqc_se=expand( + fastqc_se=lambda wildcards: expand( os.path.join( - config["output_dir"], "samples", "{sample}", "fastqc", "{mate}" + config["output_dir"], + wildcards.organism, + "samples", + "{sample}", + "fastqc", + "{mate}", + ), + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism ), - sample=pd.unique(samples_table.index.values), mate="fq1", ), - fastqc_pe=expand( + fastqc_pe=lambda wildcards: expand( os.path.join( - config["output_dir"], "samples", "{sample}", "fastqc", "{mate}" + config["output_dir"], + wildcards.organism, + "samples", + "{sample}", + "fastqc", + "{mate}", ), sample=[ i for i in pd.unique( - samples_table[samples_table["seqmode"] == "pe"].index.values + samples_table[ + (samples_table["seqmode"] == "pe") + & (samples_table["organism"] == wildcards.organism) + ].index.values ) ], mate="fq2", ), - fastqc_trimmed_se=expand( + fastqc_trimmed_se=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "fastqc_trimmed", "fq1_{seqmode}", ), zip, - sample=pd.unique(samples_table.index.values), + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), seqmode=[ get_sample("seqmode", search_id="index", search_value=i) - for i in pd.unique(samples_table.index.values) + for i in get_all_samples( + search_id="organism", search_value=wildcards.organism + ) ], ), - fastqc_trimmed_pe=expand( + fastqc_trimmed_pe=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "fastqc_trimmed", @@ -1789,59 +1991,89 @@ rule multiqc_report: sample=[ i for i in pd.unique( - samples_table[samples_table["seqmode"] == "pe"].index.values + samples_table[ + (samples_table["seqmode"] == "pe") + & (samples_table["organism"] == wildcards.organism) + ].index.values ) ], mate="fq2", ), - pseudoalignment=expand( + pseudoalignment=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "quant_kallisto", "{sample}.{seqmode}.kallisto.pseudo.sam", ), zip, - sample=[i for i in pd.unique(samples_table.index.values)], + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), seqmode=[ get_sample("seqmode", search_id="index", search_value=i) - for i in pd.unique(samples_table.index.values) + for i in get_all_samples( + search_id="organism", search_value=wildcards.organism + ) ], ), - TIN_score=expand( + TIN_score=lambda wildcards: expand( os.path.join( - config["output_dir"], "samples", "{sample}", "TIN", "TIN_score.tsv" + config["output_dir"], + wildcards.organism, + "samples", + "{sample}", + "TIN", + "TIN_score.tsv", + ), + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism ), - sample=pd.unique(samples_table.index.values), ), tables=lambda wildcards: expand( os.path.join( config["output_dir"], + wildcards.organism, "samples", "{sample}", "ALFA", "{renamed_unique}", "{sample}.ALFA_feature_counts.tsv", ), - sample=pd.unique(samples_table.index.values), + sample=get_all_samples( + search_id="organism", search_value=wildcards.organism + ), renamed_unique=alfa_dict.keys(), ), - zpca_salmon=expand( - os.path.join(config["output_dir"], "zpca", "pca_salmon_{molecule}"), + zpca_salmon=lambda wildcards: expand( + os.path.join( + config["output_dir"], + wildcards.organism, + "zpca", + "pca_salmon_{molecule}", + ), molecule=["genes", "transcripts"], ), - zpca_kallisto=expand( - os.path.join(config["output_dir"], "zpca", "pca_kallisto_{molecule}"), + zpca_kallisto=lambda wildcards: expand( + os.path.join( + config["output_dir"], + wildcards.organism, + "zpca", + "pca_kallisto_{molecule}", + ), molecule=["genes", "transcripts"], ), multiqc_config=os.path.join(config["output_dir"], "multiqc_config.yaml"), output: - multiqc_report=directory(os.path.join(config["output_dir"], "multiqc_summary")), + multiqc_report=directory( + os.path.join(config["output_dir"], "{organism}", "multiqc_summary") + ), params: cluster_log_path=config["cluster_log_dir"], results_dir=lambda wildcards, output: os.path.split(output.multiqc_report)[0], - log_dir=config["log_dir"], + log_dir=os.path.join(config["log_dir"], "{organism}"), additional_params=parse_rule_config( rule_config, current_rule=current_rule, @@ -1857,8 +2089,12 @@ rule multiqc_report: resources: mem_mb=lambda wildcards, attempt: 4096 * attempt, log: - stderr=os.path.join(config["log_dir"], f"{current_rule}.stderr.log"), - stdout=os.path.join(config["log_dir"], f"{current_rule}.stdout.log"), + stderr=os.path.join( + config["log_dir"], "{organism}", f"{current_rule}.stderr.log" + ), + stdout=os.path.join( + config["log_dir"], "{organism}", f"{current_rule}.stdout.log" + ), shell: "(multiqc \ --outdir {output.multiqc_report} \ @@ -1879,6 +2115,7 @@ rule sort_bed_4_big: input: bg=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "ALFA", @@ -1889,6 +2126,7 @@ rule sort_bed_4_big: sorted_bg=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "bigWig", @@ -1910,6 +2148,7 @@ rule sort_bed_4_big: log: stderr=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{renamed_unique}}_{{strand}}.stderr.log", @@ -1931,6 +2170,7 @@ rule prepare_bigWig: input: sorted_bg=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "bigWig", @@ -1939,7 +2179,7 @@ rule prepare_bigWig: ), chr_sizes=lambda wildcards: os.path.join( config["star_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, get_sample("index_size", search_id="index", search_value=wildcards.sample), "STAR_index", "chrNameLength.txt", @@ -1947,6 +2187,7 @@ rule prepare_bigWig: output: bigWig=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "bigWig", @@ -1967,12 +2208,14 @@ rule prepare_bigWig: log: stderr=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{renamed_unique}}_{{strand}}.stderr.log", ), stdout=os.path.join( config["log_dir"], + "{organism}", "samples", "{sample}", f"{current_rule}_{{renamed_unique}}_{{strand}}.stdout.log", diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index db88b9f..63dd06e 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -18,6 +18,12 @@ def get_sample(column_id, search_id=None, search_value=None): return str(samples_table[column_id].iloc[0]) +def get_all_samples(search_id=None, search_value=None): + return list( + pd.unique(samples_table.index[samples_table[search_id] == search_value].values) + ) + + def get_directionality(libtype, tool): """Get directionality value for different tools""" directionality = "" diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk index 06e2b49..1b86547 100644 --- a/workflow/rules/paired_end.snakefile.smk +++ b/workflow/rules/paired_end.snakefile.smk @@ -8,6 +8,7 @@ rule pe_remove_adapters_cutadapt: input: reads1=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "start", @@ -15,6 +16,7 @@ rule pe_remove_adapters_cutadapt: ), reads2=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "start", @@ -24,6 +26,7 @@ rule pe_remove_adapters_cutadapt: reads1=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.pe.remove_adapters.fastq.gz", @@ -32,6 +35,7 @@ rule pe_remove_adapters_cutadapt: reads2=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq2.pe.remove_adapters.fastq.gz", @@ -72,10 +76,18 @@ rule pe_remove_adapters_cutadapt: mem_mb=lambda wildcards, attempt: 5000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".stderr.log", ), stdout=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".stdout.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".stdout.log", ), shell: "(cutadapt \ @@ -103,12 +115,14 @@ rule pe_remove_polya_cutadapt: input: reads1=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.pe.remove_adapters.fastq.gz", ), reads2=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq2.pe.remove_adapters.fastq.gz", @@ -117,6 +131,7 @@ rule pe_remove_polya_cutadapt: reads1=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.pe.remove_polya.fastq.gz", @@ -125,6 +140,7 @@ rule pe_remove_polya_cutadapt: reads2=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq2.pe.remove_polya.fastq.gz", @@ -165,10 +181,18 @@ rule pe_remove_polya_cutadapt: mem_mb=lambda wildcards, attempt: 5000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".stderr.log", ), stdout=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".stdout.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".stdout.log", ), shell: "(cutadapt \ @@ -196,19 +220,21 @@ rule pe_map_genome_star: input: index=lambda wildcards: os.path.join( config["star_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, get_sample("index_size", search_id="index", search_value=wildcards.sample), "STAR_index", "chrNameLength.txt", ), reads1=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.pe.remove_polya.fastq.gz", ), reads2=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq2.pe.remove_polya.fastq.gz", @@ -216,6 +242,7 @@ rule pe_map_genome_star: output: bam=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", @@ -223,6 +250,7 @@ rule pe_map_genome_star: ), logfile=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", @@ -236,9 +264,7 @@ rule pe_map_genome_star: index=lambda wildcards: os.path.abspath( os.path.join( config["star_indexes"], - get_sample( - "organism", search_id="index", search_value=wildcards.sample - ), + wildcards.organism, get_sample( "index_size", search_id="index", search_value=wildcards.sample ), @@ -271,7 +297,11 @@ rule pe_map_genome_star: mem_mb=lambda wildcards, attempt: 32000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".stderr.log", ), shell: "(STAR \ @@ -299,30 +329,33 @@ rule pe_quantification_salmon: input: reads1=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.pe.remove_polya.fastq.gz", ), reads2=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq2.pe.remove_polya.fastq.gz", ), gtf=lambda wildcards: os.path.join( config["star_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, "sorted_genome.gtf", ), index=lambda wildcards: os.path.join( config["salmon_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, get_sample("kmer", search_id="index", search_value=wildcards.sample), "salmon.idx", ), output: gn_estimates=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.salmon.pe", @@ -330,6 +363,7 @@ rule pe_quantification_salmon: ), tr_estimates=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.salmon.pe", @@ -337,6 +371,7 @@ rule pe_quantification_salmon: ), meta_info=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.salmon.pe", @@ -345,6 +380,7 @@ rule pe_quantification_salmon: ), flenDist=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.salmon.pe", @@ -382,10 +418,18 @@ rule pe_quantification_salmon: mem_mb=lambda wildcards, attempt: 32000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".stderr.log", ), stdout=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".stdout.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".stdout.log", ), shell: "(salmon quant \ @@ -410,24 +454,27 @@ rule pe_genome_quantification_kallisto: input: reads1=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.pe.remove_polya.fastq.gz", ), reads2=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq2.pe.remove_polya.fastq.gz", ), index=lambda wildcards: os.path.join( config["kallisto_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, "kallisto.idx", ), output: pseudoalignment=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "quant_kallisto", @@ -435,6 +482,7 @@ rule pe_genome_quantification_kallisto: ), abundances=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "quant_kallisto", @@ -472,7 +520,11 @@ rule pe_genome_quantification_kallisto: mem_mb=lambda wildcards, attempt: 6000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".stderr.log", ), shell: "(kallisto quant \ diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk index d361ca5..5048d81 100644 --- a/workflow/rules/single_end.snakefile.smk +++ b/workflow/rules/single_end.snakefile.smk @@ -8,6 +8,7 @@ rule remove_adapters_cutadapt: input: reads=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "start", @@ -17,6 +18,7 @@ rule remove_adapters_cutadapt: reads=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.se.remove_adapters.fastq.gz", @@ -51,10 +53,18 @@ rule remove_adapters_cutadapt: mem_mb=lambda wildcards, attempt: 5000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".se.stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".se.stderr.log", ), stdout=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".se.stdout.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".se.stdout.log", ), shell: "(cutadapt \ @@ -78,6 +88,7 @@ rule remove_polya_cutadapt: input: reads=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.se.remove_adapters.fastq.gz", @@ -86,6 +97,7 @@ rule remove_polya_cutadapt: reads=temp( os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.se.remove_polya.fastq.gz", @@ -120,10 +132,18 @@ rule remove_polya_cutadapt: mem_mb=lambda wildcards, attempt: 5000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".se.stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".se.stderr.log", ), stdout=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".se.stdout.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".se.stdout.log", ), shell: "(cutadapt \ @@ -147,13 +167,14 @@ rule map_genome_star: input: index=lambda wildcards: os.path.join( config["star_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, get_sample("index_size", search_id="index", search_value=wildcards.sample), "STAR_index", "chrNameLength.txt", ), reads=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.se.remove_polya.fastq.gz", @@ -161,6 +182,7 @@ rule map_genome_star: output: bam=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", @@ -168,6 +190,7 @@ rule map_genome_star: ), logfile=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "map_genome", @@ -181,9 +204,7 @@ rule map_genome_star: index=lambda wildcards: os.path.abspath( os.path.join( config["star_indexes"], - get_sample( - "organism", search_id="index", search_value=wildcards.sample - ), + wildcards.organism, get_sample( "index_size", search_id="index", search_value=wildcards.sample ), @@ -216,7 +237,11 @@ rule map_genome_star: mem_mb=lambda wildcards, attempt: 32000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".se.stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".se.stderr.log", ), shell: "(STAR \ @@ -244,24 +269,26 @@ rule quantification_salmon: input: reads=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.se.remove_polya.fastq.gz", ), index=lambda wildcards: os.path.join( config["salmon_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, get_sample("kmer", search_id="index", search_value=wildcards.sample), "salmon.idx", ), gtf=lambda wildcards: os.path.join( config["star_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, "sorted_genome.gtf", ), output: gn_estimates=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.salmon.se", @@ -269,6 +296,7 @@ rule quantification_salmon: ), tr_estimates=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.salmon.se", @@ -276,6 +304,7 @@ rule quantification_salmon: ), meta_info=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.salmon.se", @@ -284,6 +313,7 @@ rule quantification_salmon: ), flenDist=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.salmon.se", @@ -326,10 +356,18 @@ rule quantification_salmon: mem_mb=lambda wildcards, attempt: 32000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".se.stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".se.stderr.log", ), stdout=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".se.stdout.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".se.stdout.log", ), shell: "(salmon quant \ @@ -355,18 +393,20 @@ rule genome_quantification_kallisto: input: reads=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "{sample}.fq1.se.remove_polya.fastq.gz", ), index=lambda wildcards: os.path.join( config["kallisto_indexes"], - get_sample("organism", search_id="index", search_value=wildcards.sample), + wildcards.organism, "kallisto.idx", ), output: pseudoalignment=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "quant_kallisto", @@ -374,6 +414,7 @@ rule genome_quantification_kallisto: ), abundances=os.path.join( config["output_dir"], + "{organism}", "samples", "{sample}", "quant_kallisto", @@ -417,7 +458,11 @@ rule genome_quantification_kallisto: mem_mb=lambda wildcards, attempt: 6000 * attempt, log: stderr=os.path.join( - config["log_dir"], "samples", "{sample}", current_rule + ".se.stderr.log" + config["log_dir"], + "{organism}", + "samples", + "{sample}", + current_rule + ".se.stderr.log", ), shell: "(kallisto quant \