| endogenous_count_barplot |
1 |
- output/results/endogenous/summary.png
|
|
|
| task_endogenous_count_barplot.py \
-i {input} \
-o {output}
|
|
| preprocess_stats |
1 |
- output/results/qc/preprocess.tsv
- output/results/qc/preprocess_barplot.png
|
|
|
| task_preprocess_stats.py \
--log-file {input.logs} \
--sample-names {params.samples} \
--output-tsv {output.tsv} \
--output-plot {output.plot}
|
|
| fastqc |
6 |
- output/results/qc/SRR8114380_SE_fastqc/Images/per_base_quality.png
- output/results/qc/SRR8114381_SE_fastqc/Images/per_base_quality.png
- output/results/qc/SRR8114382_SE_fastqc/Images/per_base_quality.png
- output/results/qc/SRR8114383_SE_fastqc/Images/per_base_quality.png
- output/results/qc/SRR8114384_SE_fastqc/Images/per_base_quality.png
- output/results/qc/SRR8114385_SE_fastqc/Images/per_base_quality.png
|
|
|
| fastqc -o {params.outdir} {input.fastq}
unzip {params.outdir}/{wildcards.sample}_SE_fastqc.zip \
-d {params.outdir}/
rm -rf {params.outdir}/{wildcards.sample}_SE_fastqc.zip
|
|
| organize_exogenous |
1 |
- output/results/silva/
- output/results/bacteria/
|
|
|
| cp -r {input.silva} {output.silva}
cp -r {input.bacteria} {output.bacteria}
|
|
| organize_endogenous_counts |
1 |
- output/results/endogenous/ReadsPerGene_gencode.txt
- output/results/endogenous/ReadsPerGene_tRNA.txt
- output/results/endogenous/ReadsPerGene_piRNA.txt
- output/results/endogenous/ReadsPerGene_summary.txt
|
|
|
| cp {input.gencode} {output.gencode}
cp {input.tRNA} {output.tRNA}
cp {input.piRNA} {output.piRNA}
cp {input.summary} {output.summary}
|
|
| preprocess |
6 |
- output/01-Preprocess/SRR8114380/SRR8114380_SE.fastq.gz
- output/01-Preprocess/SRR8114380/SRR8114380.htsStats.log
- output/01-Preprocess/SRR8114381/SRR8114381_SE.fastq.gz
- output/01-Preprocess/SRR8114381/SRR8114381.htsStats.log
- output/01-Preprocess/SRR8114382/SRR8114382_SE.fastq.gz
- output/01-Preprocess/SRR8114382/SRR8114382.htsStats.log
- output/01-Preprocess/SRR8114383/SRR8114383_SE.fastq.gz
- output/01-Preprocess/SRR8114383/SRR8114383.htsStats.log
- output/01-Preprocess/SRR8114384/SRR8114384_SE.fastq.gz
- output/01-Preprocess/SRR8114384/SRR8114384.htsStats.log
- output/01-Preprocess/SRR8114385/SRR8114385_SE.fastq.gz
- output/01-Preprocess/SRR8114385/SRR8114385.htsStats.log
|
|
|
| task_preprocess.py \
--input-fq {input.sample} \
--output-fq {output.fastq} \
--sample-name {wildcards.sample} \
--prefix {params.prefix} \
--adapter {params.adapter} \
--log-file {output.log} \
--scratch-dir {params.scratch}
|
|
| silva_count_combine |
6 |
- output/06-SILVA/SILVA_count_phylum.txt
- output/06-SILVA/SILVA_count_class.txt
- output/06-SILVA/SILVA_count_order.txt
- output/06-SILVA/SILVA_count_family.txt
- output/06-SILVA/SILVA_count_genus.txt
- output/06-SILVA/SILVA_count_species.txt
|
|
|
|
| bacteria_count_combine |
6 |
- output/07-Bacteria/bacteria_count_phylum.txt
- output/07-Bacteria/bacteria_count_class.txt
- output/07-Bacteria/bacteria_count_order.txt
- output/07-Bacteria/bacteria_count_family.txt
- output/07-Bacteria/bacteria_count_genus.txt
- output/07-Bacteria/bacteria_count_species.txt
|
|
|
|
| summarize_counts |
1 |
- output/04-Genome/ReadsPerGene_gencode.txt
- output/04-Genome/ReadsPerGene_tRNA.txt
- output/04-Genome/ReadsPerGene_piRNA.txt
- output/04-Genome/ReadsPerGene_summary.txt
|
|
|
| task_summarize_counts.py \
--input-gencode {input.gencode} \
--input-tRNA {input.tRNA} \
--input-piRNA {input.piRNA} \
--output-gencode {output.gencode} \
--output-tRNA {output.tRNA} \
--output-piRNA {output.piRNA} \
--output-summary {output.summary} \
--sample-names {params.samples}
|
|
| silva_count_taxa |
6 |
- output/06-SILVA/SRR8114380/exogenousAligned_SILVA_phylum.txt
- output/06-SILVA/SRR8114380/exogenousAligned_SILVA_class.txt
- output/06-SILVA/SRR8114380/exogenousAligned_SILVA_order.txt
- output/06-SILVA/SRR8114380/exogenousAligned_SILVA_family.txt
- output/06-SILVA/SRR8114380/exogenousAligned_SILVA_genus.txt
- output/06-SILVA/SRR8114380/exogenousAligned_SILVA_species.txt
- output/06-SILVA/SRR8114381/exogenousAligned_SILVA_phylum.txt
- output/06-SILVA/SRR8114381/exogenousAligned_SILVA_class.txt
- output/06-SILVA/SRR8114381/exogenousAligned_SILVA_order.txt
- output/06-SILVA/SRR8114381/exogenousAligned_SILVA_family.txt
- output/06-SILVA/SRR8114381/exogenousAligned_SILVA_genus.txt
- output/06-SILVA/SRR8114381/exogenousAligned_SILVA_species.txt
- output/06-SILVA/SRR8114382/exogenousAligned_SILVA_phylum.txt
- output/06-SILVA/SRR8114382/exogenousAligned_SILVA_class.txt
- output/06-SILVA/SRR8114382/exogenousAligned_SILVA_order.txt
- output/06-SILVA/SRR8114382/exogenousAligned_SILVA_family.txt
- output/06-SILVA/SRR8114382/exogenousAligned_SILVA_genus.txt
- output/06-SILVA/SRR8114382/exogenousAligned_SILVA_species.txt
- output/06-SILVA/SRR8114383/exogenousAligned_SILVA_phylum.txt
- output/06-SILVA/SRR8114383/exogenousAligned_SILVA_class.txt
- output/06-SILVA/SRR8114383/exogenousAligned_SILVA_order.txt
- output/06-SILVA/SRR8114383/exogenousAligned_SILVA_family.txt
- output/06-SILVA/SRR8114383/exogenousAligned_SILVA_genus.txt
- output/06-SILVA/SRR8114383/exogenousAligned_SILVA_species.txt
- output/06-SILVA/SRR8114384/exogenousAligned_SILVA_phylum.txt
- output/06-SILVA/SRR8114384/exogenousAligned_SILVA_class.txt
- output/06-SILVA/SRR8114384/exogenousAligned_SILVA_order.txt
- output/06-SILVA/SRR8114384/exogenousAligned_SILVA_family.txt
- output/06-SILVA/SRR8114384/exogenousAligned_SILVA_genus.txt
- output/06-SILVA/SRR8114384/exogenousAligned_SILVA_species.txt
- output/06-SILVA/SRR8114385/exogenousAligned_SILVA_phylum.txt
- output/06-SILVA/SRR8114385/exogenousAligned_SILVA_class.txt
- output/06-SILVA/SRR8114385/exogenousAligned_SILVA_order.txt
- output/06-SILVA/SRR8114385/exogenousAligned_SILVA_family.txt
- output/06-SILVA/SRR8114385/exogenousAligned_SILVA_genus.txt
- output/06-SILVA/SRR8114385/exogenousAligned_SILVA_species.txt
|
|
|
| task_count_exogenous_taxa.py \
--input-file {input.sample} \
--output-prefix {params.prefix} \
--nodes-dmp {input.taxdump}/nodes.dmp \
--names-dmp {input.taxdump}/names.dmp
|
|
| bacteria_count_taxa |
6 |
- output/07-Bacteria/SRR8114380/exogenousAligned_bacteria_phylum.txt
- output/07-Bacteria/SRR8114380/exogenousAligned_bacteria_class.txt
- output/07-Bacteria/SRR8114380/exogenousAligned_bacteria_order.txt
- output/07-Bacteria/SRR8114380/exogenousAligned_bacteria_family.txt
- output/07-Bacteria/SRR8114380/exogenousAligned_bacteria_genus.txt
- output/07-Bacteria/SRR8114380/exogenousAligned_bacteria_species.txt
- output/07-Bacteria/SRR8114381/exogenousAligned_bacteria_phylum.txt
- output/07-Bacteria/SRR8114381/exogenousAligned_bacteria_class.txt
- output/07-Bacteria/SRR8114381/exogenousAligned_bacteria_order.txt
- output/07-Bacteria/SRR8114381/exogenousAligned_bacteria_family.txt
- output/07-Bacteria/SRR8114381/exogenousAligned_bacteria_genus.txt
- output/07-Bacteria/SRR8114381/exogenousAligned_bacteria_species.txt
- output/07-Bacteria/SRR8114382/exogenousAligned_bacteria_phylum.txt
- output/07-Bacteria/SRR8114382/exogenousAligned_bacteria_class.txt
- output/07-Bacteria/SRR8114382/exogenousAligned_bacteria_order.txt
- output/07-Bacteria/SRR8114382/exogenousAligned_bacteria_family.txt
- output/07-Bacteria/SRR8114382/exogenousAligned_bacteria_genus.txt
- output/07-Bacteria/SRR8114382/exogenousAligned_bacteria_species.txt
- output/07-Bacteria/SRR8114383/exogenousAligned_bacteria_phylum.txt
- output/07-Bacteria/SRR8114383/exogenousAligned_bacteria_class.txt
- output/07-Bacteria/SRR8114383/exogenousAligned_bacteria_order.txt
- output/07-Bacteria/SRR8114383/exogenousAligned_bacteria_family.txt
- output/07-Bacteria/SRR8114383/exogenousAligned_bacteria_genus.txt
- output/07-Bacteria/SRR8114383/exogenousAligned_bacteria_species.txt
- output/07-Bacteria/SRR8114384/exogenousAligned_bacteria_phylum.txt
- output/07-Bacteria/SRR8114384/exogenousAligned_bacteria_class.txt
- output/07-Bacteria/SRR8114384/exogenousAligned_bacteria_order.txt
- output/07-Bacteria/SRR8114384/exogenousAligned_bacteria_family.txt
- output/07-Bacteria/SRR8114384/exogenousAligned_bacteria_genus.txt
- output/07-Bacteria/SRR8114384/exogenousAligned_bacteria_species.txt
- output/07-Bacteria/SRR8114385/exogenousAligned_bacteria_phylum.txt
- output/07-Bacteria/SRR8114385/exogenousAligned_bacteria_class.txt
- output/07-Bacteria/SRR8114385/exogenousAligned_bacteria_order.txt
- output/07-Bacteria/SRR8114385/exogenousAligned_bacteria_family.txt
- output/07-Bacteria/SRR8114385/exogenousAligned_bacteria_genus.txt
- output/07-Bacteria/SRR8114385/exogenousAligned_bacteria_species.txt
|
|
|
| task_count_exogenous_taxa.py \
--input-file {input.sample} \
--output-prefix {params.prefix} \
--nodes-dmp {input.taxdump}/nodes.dmp \
--names-dmp {input.taxdump}/names.dmp
|
|
| endogenous_count |
6 |
- output/04-Genome/SRR8114380/ReadsPerGene_gencode.txt
- output/04-Genome/SRR8114380/ReadsPerGene_tRNA.txt
- output/04-Genome/SRR8114380/ReadsPerGene_piRNA.txt
- output/04-Genome/SRR8114381/ReadsPerGene_gencode.txt
- output/04-Genome/SRR8114381/ReadsPerGene_tRNA.txt
- output/04-Genome/SRR8114381/ReadsPerGene_piRNA.txt
- output/04-Genome/SRR8114382/ReadsPerGene_gencode.txt
- output/04-Genome/SRR8114382/ReadsPerGene_tRNA.txt
- output/04-Genome/SRR8114382/ReadsPerGene_piRNA.txt
- output/04-Genome/SRR8114383/ReadsPerGene_gencode.txt
- output/04-Genome/SRR8114383/ReadsPerGene_tRNA.txt
- output/04-Genome/SRR8114383/ReadsPerGene_piRNA.txt
- output/04-Genome/SRR8114384/ReadsPerGene_gencode.txt
- output/04-Genome/SRR8114384/ReadsPerGene_tRNA.txt
- output/04-Genome/SRR8114384/ReadsPerGene_piRNA.txt
- output/04-Genome/SRR8114385/ReadsPerGene_gencode.txt
- output/04-Genome/SRR8114385/ReadsPerGene_tRNA.txt
- output/04-Genome/SRR8114385/ReadsPerGene_piRNA.txt
|
|
|
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16 | htseq-count -f bam -s no -i gene_id \
--additional-attr gene_name --additional-attr gene_type \
{input.bam} \
{input.gencode} \
> {output.gencode}
htseq-count -f bam -s no -i gene_id \
--additional-attr gene_name --additional-attr gene_type \
{input.bam} \
{input.tRNA} \
> {output.tRNA}
htseq-count -f bam -s no -i gene_id \
--additional-attr gene_name --additional-attr gene_type \
{input.bam} \
{input.piRNA} \
> {output.piRNA}
|
|
| silva_combine |
6 |
- output/06-SILVA/SRR8114380/Aligned_combine.txt.gz
- output/06-SILVA/SRR8114381/Aligned_combine.txt.gz
- output/06-SILVA/SRR8114382/Aligned_combine.txt.gz
- output/06-SILVA/SRR8114383/Aligned_combine.txt.gz
- output/06-SILVA/SRR8114384/Aligned_combine.txt.gz
- output/06-SILVA/SRR8114385/Aligned_combine.txt.gz
|
|
|
| zcat {input} |
gzip -c > {output}
|
|
| bacteria_combine_result |
6 |
- output/07-Bacteria/SRR8114380/Aligned.txt.gz
- output/07-Bacteria/SRR8114381/Aligned.txt.gz
- output/07-Bacteria/SRR8114382/Aligned.txt.gz
- output/07-Bacteria/SRR8114383/Aligned.txt.gz
- output/07-Bacteria/SRR8114384/Aligned.txt.gz
- output/07-Bacteria/SRR8114385/Aligned.txt.gz
|
|
|
| zcat {input} | \
awk -F ' ' '{{split($2, taxa, ":"); print($1" "taxa[1])}}' | \
uniq | gzip \
> {output}
|
|
| genome_mapping |
6 |
- output/04-Genome/SRR8114380/Aligned.out.bam
- output/04-Genome/SRR8114380/Unmapped.fastq.gz
- output/04-Genome/SRR8114381/Aligned.out.bam
- output/04-Genome/SRR8114381/Unmapped.fastq.gz
- output/04-Genome/SRR8114382/Aligned.out.bam
- output/04-Genome/SRR8114382/Unmapped.fastq.gz
- output/04-Genome/SRR8114383/Aligned.out.bam
- output/04-Genome/SRR8114383/Unmapped.fastq.gz
- output/04-Genome/SRR8114384/Aligned.out.bam
- output/04-Genome/SRR8114384/Unmapped.fastq.gz
- output/04-Genome/SRR8114385/Aligned.out.bam
- output/04-Genome/SRR8114385/Unmapped.fastq.gz
|
|
|
| task_star_align.py \
-i {input.sample} \
-g {input.genome} \
-n {wildcards.sample} \
-b {output.bam} \
-u {output.unmapped} \
-p {params.prefix} \
-t {threads} \
-s {params.scratch}
|
|
| silva_mapping |
60 |
- output/06-SILVA/SRR8114380/Aligned_1.txt.gz
- output/06-SILVA/SRR8114380/Aligned_2.txt.gz
- output/06-SILVA/SRR8114380/Aligned_3.txt.gz
- output/06-SILVA/SRR8114380/Aligned_4.txt.gz
- output/06-SILVA/SRR8114380/Aligned_5.txt.gz
- output/06-SILVA/SRR8114380/Aligned_6.txt.gz
- output/06-SILVA/SRR8114380/Aligned_7.txt.gz
- output/06-SILVA/SRR8114380/Aligned_8.txt.gz
- output/06-SILVA/SRR8114380/Aligned_9.txt.gz
- output/06-SILVA/SRR8114380/Aligned_10.txt.gz
- output/06-SILVA/SRR8114381/Aligned_1.txt.gz
- output/06-SILVA/SRR8114381/Aligned_2.txt.gz
- output/06-SILVA/SRR8114381/Aligned_3.txt.gz
- output/06-SILVA/SRR8114381/Aligned_4.txt.gz
- output/06-SILVA/SRR8114381/Aligned_5.txt.gz
- output/06-SILVA/SRR8114381/Aligned_6.txt.gz
- output/06-SILVA/SRR8114381/Aligned_7.txt.gz
- output/06-SILVA/SRR8114381/Aligned_8.txt.gz
- output/06-SILVA/SRR8114381/Aligned_9.txt.gz
- output/06-SILVA/SRR8114381/Aligned_10.txt.gz
- output/06-SILVA/SRR8114382/Aligned_1.txt.gz
- output/06-SILVA/SRR8114382/Aligned_2.txt.gz
- output/06-SILVA/SRR8114382/Aligned_3.txt.gz
- output/06-SILVA/SRR8114382/Aligned_4.txt.gz
- output/06-SILVA/SRR8114382/Aligned_5.txt.gz
- output/06-SILVA/SRR8114382/Aligned_6.txt.gz
- output/06-SILVA/SRR8114382/Aligned_7.txt.gz
- output/06-SILVA/SRR8114382/Aligned_8.txt.gz
- output/06-SILVA/SRR8114382/Aligned_9.txt.gz
- output/06-SILVA/SRR8114382/Aligned_10.txt.gz
- output/06-SILVA/SRR8114383/Aligned_1.txt.gz
- output/06-SILVA/SRR8114383/Aligned_2.txt.gz
- output/06-SILVA/SRR8114383/Aligned_3.txt.gz
- output/06-SILVA/SRR8114383/Aligned_4.txt.gz
- output/06-SILVA/SRR8114383/Aligned_5.txt.gz
- output/06-SILVA/SRR8114383/Aligned_6.txt.gz
- output/06-SILVA/SRR8114383/Aligned_7.txt.gz
- output/06-SILVA/SRR8114383/Aligned_8.txt.gz
- output/06-SILVA/SRR8114383/Aligned_9.txt.gz
- output/06-SILVA/SRR8114383/Aligned_10.txt.gz
- output/06-SILVA/SRR8114384/Aligned_1.txt.gz
- output/06-SILVA/SRR8114384/Aligned_2.txt.gz
- output/06-SILVA/SRR8114384/Aligned_3.txt.gz
- output/06-SILVA/SRR8114384/Aligned_4.txt.gz
- output/06-SILVA/SRR8114384/Aligned_5.txt.gz
- output/06-SILVA/SRR8114384/Aligned_6.txt.gz
- output/06-SILVA/SRR8114384/Aligned_7.txt.gz
- output/06-SILVA/SRR8114384/Aligned_8.txt.gz
- output/06-SILVA/SRR8114384/Aligned_9.txt.gz
- output/06-SILVA/SRR8114384/Aligned_10.txt.gz
- output/06-SILVA/SRR8114385/Aligned_1.txt.gz
- output/06-SILVA/SRR8114385/Aligned_2.txt.gz
- output/06-SILVA/SRR8114385/Aligned_3.txt.gz
- output/06-SILVA/SRR8114385/Aligned_4.txt.gz
- output/06-SILVA/SRR8114385/Aligned_5.txt.gz
- output/06-SILVA/SRR8114385/Aligned_6.txt.gz
- output/06-SILVA/SRR8114385/Aligned_7.txt.gz
- output/06-SILVA/SRR8114385/Aligned_8.txt.gz
- output/06-SILVA/SRR8114385/Aligned_9.txt.gz
- output/06-SILVA/SRR8114385/Aligned_10.txt.gz
|
|
|
| task_star_align_silva.py \
-i {input.sample} \
-n {wildcards.sample} \
-c {wildcards.silva_ind} \
-g {input.genome} \
-o {output} \
-p {params.prefix} \
-t {threads} \
-s {params.scratch}
|
|
| bacteria_mapping |
1104 |
|
|
|
| task_star_align_bacteria.py \
-i {input.sample} \
-n {wildcards.sample} \
-c {wildcards.bacteria_ind} \
-g {input.genome} \
-o {output} \
-p {params.prefix} \
-t {threads} \
-s {params.scratch}
|
|
| rrna_mapping |
6 |
- output/03-rRNA/SRR8114380/Aligned.out.bam
- output/03-rRNA/SRR8114380/Unmapped.fastq.gz
- output/03-rRNA/SRR8114381/Aligned.out.bam
- output/03-rRNA/SRR8114381/Unmapped.fastq.gz
- output/03-rRNA/SRR8114382/Aligned.out.bam
- output/03-rRNA/SRR8114382/Unmapped.fastq.gz
- output/03-rRNA/SRR8114383/Aligned.out.bam
- output/03-rRNA/SRR8114383/Unmapped.fastq.gz
- output/03-rRNA/SRR8114384/Aligned.out.bam
- output/03-rRNA/SRR8114384/Unmapped.fastq.gz
- output/03-rRNA/SRR8114385/Aligned.out.bam
- output/03-rRNA/SRR8114385/Unmapped.fastq.gz
|
|
|
| task_star_align.py \
-i {input.sample} \
-g {input.genome} \
-n {wildcards.sample} \
-b {output.bam} \
-u {output.unmapped} \
-p {params.prefix} \
-t {threads} \
-s {params.scratch}
|
|
| re_mapping |
6 |
- output/05-RE/SRR8114380/Aligned.out.bam
- output/05-RE/SRR8114380/Unmapped.fastq.gz
- output/05-RE/SRR8114381/Aligned.out.bam
- output/05-RE/SRR8114381/Unmapped.fastq.gz
- output/05-RE/SRR8114382/Aligned.out.bam
- output/05-RE/SRR8114382/Unmapped.fastq.gz
- output/05-RE/SRR8114383/Aligned.out.bam
- output/05-RE/SRR8114383/Unmapped.fastq.gz
- output/05-RE/SRR8114384/Aligned.out.bam
- output/05-RE/SRR8114384/Unmapped.fastq.gz
- output/05-RE/SRR8114385/Aligned.out.bam
- output/05-RE/SRR8114385/Unmapped.fastq.gz
|
|
|
| task_star_align.py \
-i {input.sample} \
-g {input.genome} \
-n {wildcards.sample} \
-b {output.bam} \
-u {output.unmapped} \
-p {params.prefix} \
-t {threads} \
-s {params.scratch}
|
|
| silva_index |
10 |
- genomes/silva_tax/star_index_silva_1
- genomes/silva_tax/star_index_silva_2
- genomes/silva_tax/star_index_silva_3
- genomes/silva_tax/star_index_silva_4
- genomes/silva_tax/star_index_silva_5
- genomes/silva_tax/star_index_silva_6
- genomes/silva_tax/star_index_silva_7
- genomes/silva_tax/star_index_silva_8
- genomes/silva_tax/star_index_silva_9
- genomes/silva_tax/star_index_silva_10
|
|
|
| task_star_index.py \
-i {input.genome} \
-o {output} \
-t {threads} \
-m {params.mem} \
-a "{params.extra}" \
-s {params.scratch}
|
|
| bacteria_index |
184 |
|
|
|
| task_star_index.py \
-i {input.genome} \
-o {output} \
-t {threads} \
-m {params.mem} \
-a "{params.extra}" \
-s {params.scratch}
|
|
| silva_extract_unmapped |
6 |
- output/06-SILVA/SRR8114380/Unmapped.fastq.gz
- output/06-SILVA/SRR8114381/Unmapped.fastq.gz
- output/06-SILVA/SRR8114382/Unmapped.fastq.gz
- output/06-SILVA/SRR8114383/Unmapped.fastq.gz
- output/06-SILVA/SRR8114384/Unmapped.fastq.gz
- output/06-SILVA/SRR8114385/Unmapped.fastq.gz
|
|
|
| task_silva_extract_unmapped.py \
-a {input.aligned} \
-u {input.fastq} \
-o {output.unmapped} \
-l {params.namelist_path} \
-s {params.scratch}
|
|
| rrna_index |
1 |
- genomes/star_index_rrna_human
|
|
|
| task_star_index.py \
-i {input.genome} \
-o {output} \
-t {threads} \
-m {params.mem} \
-a "{params.extra}" \
-s {params.scratch}
|
|
| univec_mapping |
6 |
- output/02-UniVec/SRR8114380/Aligned.out.bam
- output/02-UniVec/SRR8114380/Unmapped.fastq.gz
- output/02-UniVec/SRR8114381/Aligned.out.bam
- output/02-UniVec/SRR8114381/Unmapped.fastq.gz
- output/02-UniVec/SRR8114382/Aligned.out.bam
- output/02-UniVec/SRR8114382/Unmapped.fastq.gz
- output/02-UniVec/SRR8114383/Aligned.out.bam
- output/02-UniVec/SRR8114383/Unmapped.fastq.gz
- output/02-UniVec/SRR8114384/Aligned.out.bam
- output/02-UniVec/SRR8114384/Unmapped.fastq.gz
- output/02-UniVec/SRR8114385/Aligned.out.bam
- output/02-UniVec/SRR8114385/Unmapped.fastq.gz
|
|
|
| task_star_align.py \
-i {input.sample} \
-g {input.genome} \
-n {wildcards.sample} \
-b {output.bam} \
-u {output.unmapped} \
-p {params.prefix} \
-t {threads} \
-s {params.scratch}
|
|
| re_index |
1 |
|
|
|
| task_star_index.py \
-i {input.genome} \
-o {output} \
-t {threads} \
-m {params.mem} \
-a "{params.extra}" \
-s {params.scratch}
|
|
| make_silva |
1 |
- genomes/silva_filter_ncbiTaxa.fasta
- genomes/silva_tax/silva_1.fasta
- genomes/silva_tax/silva_2.fasta
- genomes/silva_tax/silva_3.fasta
- genomes/silva_tax/silva_4.fasta
- genomes/silva_tax/silva_5.fasta
- genomes/silva_tax/silva_6.fasta
- genomes/silva_tax/silva_7.fasta
- genomes/silva_tax/silva_8.fasta
- genomes/silva_tax/silva_9.fasta
- genomes/silva_tax/silva_10.fasta
|
|
|
| zcat {input} | sed -E 's/ .+$/:SSU/' > {output.combine}
task_split_fasta.py \
--input-file {output.combine} \
--output-prefix {params.output_prefix} \
--n-batch {params.parallel}
|
|
| bacteria_combine_genome |
184 |
|
|
|
| for fa in $(find "{input.genome_collection}" -name "*.dna.toplevel.fa.gz")
do
taxa=$(basename -- $fa |cut -d '.' -f1)
zcat $fa | sed "s/^>/>$taxa:/g" >> {output}
done
|
|
| univec_index |
1 |
- genomes/star_index_univec
|
|
|
| task_star_index.py \
-i {input.genome} \
-o {output} \
-t {threads} \
-m {params.mem} \
-a "{params.extra}" \
-s {params.scratch}
|
|
| solve_silva_taxa |
2 |
- genomes/silva_ssu_filter_ncbiTaxa.fa.gz
- genomes/silva_lsu_filter_ncbiTaxa.fa.gz
|
|
|
| task_solve_silva_taxa.py \
-f {input.fasta} \
-t {input.taxmap} \
-s {wildcards.su} \
-o {output}
|
|
| filter_silva |
1 |
- genomes/silva_lsu_filter.fa.gz
- genomes/silva_ssu_filter.fa.gz
- genomes/silva_lsu_namelist.txt
- genomes/silva_ssu_namelist.txt
|
|
|
1
2
3
4
5
6
7
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9
10
11
12
13
14
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16
17
18
19
20
21 | zcat {input.silva_lsu} | grep '^>' |\
grep -e ' Bacteria;' -e ' Archaea;' \
-e ' Eukaryota;Opisthokonta;Nucletmycea;Fungi;' |\
sed 's/^>//g' > {output.silva_lsu_namelist}
zcat {input.silva_ssu} | grep '^>' |\
grep -e ' Bacteria;' -e ' Archaea;' \
-e ' Eukaryota;Opisthokonta;Nucletmycea;Fungi;' |\
sed 's/^>//g' > {output.silva_ssu_namelist}
task_extract_fastx.py \
--input-file {input.silva_lsu} \
--output-file {output.silva_lsu} \
--namelist-file {output.silva_lsu_namelist} \
--seq-format fasta \
--verbose
task_extract_fastx.py \
--input-file {input.silva_ssu} \
--output-file {output.silva_ssu} \
--namelist-file {output.silva_ssu_namelist} \
--seq-format fasta \
--verbose
|
|
| download_silva |
1 |
- genomes/silva_lsu.fa.gz
- genomes/silva_ssu.fa.gz
- genomes/silva_lsu_taxmap.txt
- genomes/silva_ssu_taxmap.txt
|
|
|
| wget {params.lsu} -O genomes/silva_lsu.fa.gz
wget {params.ssu} -O genomes/silva_ssu.fa.gz
wget {params.taxmap_lsu} -O genomes/silva_taxmap_lsu.txt.gz
zcat genomes/silva_taxmap_lsu.txt.gz > {output.taxmap_lsu}
wget {params.taxmap_ssu} -O genomes/silva_taxmap_ssu.txt.gz
zcat genomes/silva_taxmap_ssu.txt.gz > {output.taxmap_ssu}
|
|