Workflow

Detailed software versions can be found under Rules.

Results

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Rules

Workflow rules
Rule Jobs Output Singularity Conda environment Code
make_bedgraph_plus 2
  • vignette/output/WTnone/plus.bedgraph
  • vignette/output/WT3AT/plus.bedgraph
1
bedtools --version &> {log}; bedtools genomecov -ibam {input.bam} -trackline -bga -5 -strand + > {output} 2>> {log}
make_bedgraph_minus 2
  • vignette/output/WTnone/minus.bedgraph
  • vignette/output/WT3AT/minus.bedgraph
1
bedtools --version &> {log}; bedtools genomecov -ibam {input.bam} -trackline -bga -5 -strand - > {output} 2>> {log}
collate_tpms 1
  • vignette/output/TPMs_collated.tsv
1
Rscript --vanilla rscripts/collate_tpms.R --sample-subdirs=True --output-dir={config[dir_out]} WTnone WT3AT &> {log}
count_reads 1
  • vignette/output/read_counts.tsv
1
python -m riboviz.tools.count_reads -c {input} -i {config[dir_in]} -t {config[dir_tmp]} -o {config[dir_out]} -r {output} &> {log}
sort_bam 2
  • vignette/output/WTnone/WTnone.bam
  • vignette/output/WT3AT/WT3AT.bam
1
samtools --version &> {log}; samtools view -b {input} | samtools sort -@ {config[num_processes]} -O bam -o {output} - &>> {log}
index_bam 2
  • vignette/output/WTnone/WTnone.bam.bai
  • vignette/output/WT3AT/WT3AT.bam.bai
1
samtools --version &> {log}; samtools index {input} &>> {log}
generate_stats_figs 2
  • vignette/output/WTnone/3nt_periodicity.tsv
  • vignette/output/WTnone/3nt_periodicity.pdf
  • vignette/output/WTnone/read_lengths.tsv
  • vignette/output/WTnone/read_lengths.pdf
  • vignette/output/WTnone/pos_sp_nt_freq.tsv
  • vignette/output/WTnone/pos_sp_rpf_norm_reads.pdf
  • vignette/output/WTnone/pos_sp_rpf_norm_reads.tsv
  • vignette/output/WTnone/features.pdf
  • vignette/output/WTnone/tpms.tsv
  • vignette/output/WTnone/codon_ribodens.tsv
  • vignette/output/WTnone/codon_ribodens.pdf
  • vignette/output/WTnone/startcodon_ribogridbar.pdf
  • vignette/output/WTnone/startcodon_ribogrid.pdf
  • vignette/output/WTnone/3ntframe_bygene.tsv
  • vignette/output/WTnone/3ntframe_propbygene.pdf
  • vignette/output/WT3AT/3nt_periodicity.tsv
  • vignette/output/WT3AT/3nt_periodicity.pdf
  • vignette/output/WT3AT/read_lengths.tsv
  • vignette/output/WT3AT/read_lengths.pdf
  • vignette/output/WT3AT/pos_sp_nt_freq.tsv
  • vignette/output/WT3AT/pos_sp_rpf_norm_reads.pdf
  • vignette/output/WT3AT/pos_sp_rpf_norm_reads.tsv
  • vignette/output/WT3AT/features.pdf
  • vignette/output/WT3AT/tpms.tsv
  • vignette/output/WT3AT/codon_ribodens.tsv
  • vignette/output/WT3AT/codon_ribodens.pdf
  • vignette/output/WT3AT/startcodon_ribogridbar.pdf
  • vignette/output/WT3AT/startcodon_ribogrid.pdf
  • vignette/output/WT3AT/3ntframe_bygene.tsv
  • vignette/output/WT3AT/3ntframe_propbygene.pdf
1
Rscript --vanilla rscripts/generate_stats_figs.R --num-processes={config[num_processes]} --min-read-length={config[min_read_length]} --max-read-length={config[max_read_length]} --buffer={config[buffer]} --primary-id={config[primary_id]} --dataset={config[dataset]} --hd-file={input.h5} --orf-fasta-file={input.fasta} --rpf={config[rpf]} --output-dir={params.output_dir} --do-pos-sp-nt-freq={config[do_pos_sp_nt_freq]} --t-rna-file={input.t_rna} --codon-positions-file={input.codon_positions} --features-file={input.features} --orf-gff-file={input.gff} --asite-disp-length-file={input.asite_disp_length} --count-threshold={config[count_threshold]} &> {log}
make_sample_sheet 1
  • vignette/output/sample_sheet.yaml
source
trim_5p_mismatches 2
  • vignette/tmp/WTnone/orf_map_clean.sam
  • vignette/tmp/WTnone/trim_5p_mismatch.tsv
  • vignette/tmp/WT3AT/orf_map_clean.sam
  • vignette/tmp/WT3AT/trim_5p_mismatch.tsv
1
python -m riboviz.tools.trim_5p_mismatch -m 2 -i {input} -o {output.clean_sam} -s {output.tsv} &> {log}
bam_to_h5 2
  • vignette/output/WTnone/WTnone.h5
  • vignette/output/WT3AT/WT3AT.h5
1
Rscript --vanilla rscripts/bam_to_h5.R --num-processes={config[num_processes]} --min-read-length={config[min_read_length]} --max-read-length={config[max_read_length]} --buffer={config[buffer]} --primary-id={config[primary_id]} --secondary-id={params.secondary_id} --dataset={config[dataset]} --bam-file={input.bam} --hd-file={output} --orf-gff-file={input.gff} --is-riboviz-gff={config[is_riboviz_gff]} --stop-in-cds={config[stop_in_cds]} &> {log}
map_to_orf 2
  • vignette/tmp/WTnone/unaligned.fq
  • vignette/tmp/WTnone/orf_map.sam
  • vignette/tmp/WT3AT/unaligned.fq
  • vignette/tmp/WT3AT/orf_map.sam
1
hisat2 --version &> {log}; hisat2 -p {config[num_processes]} -k 2 --no-spliced-alignment --rna-strandness F --no-unal --un {output.fq} -x {params.prefix} -S {output.sam} -U {input.fq} &>> {log}
build_indices_orf 1
  • vignette/index/YAL_CDS_w_250.1.ht2
  • vignette/index/YAL_CDS_w_250.2.ht2
  • vignette/index/YAL_CDS_w_250.3.ht2
  • vignette/index/YAL_CDS_w_250.4.ht2
  • vignette/index/YAL_CDS_w_250.5.ht2
  • vignette/index/YAL_CDS_w_250.6.ht2
  • vignette/index/YAL_CDS_w_250.7.ht2
  • vignette/index/YAL_CDS_w_250.8.ht2
1
hisat2-build --version &> {log}; hisat2-build {input} {params.prefix} &>> {log}
map_to_r_rna 2
  • vignette/tmp/WTnone/nonrRNA.fq
  • vignette/tmp/WTnone/rRNA_map.sam
  • vignette/tmp/WT3AT/nonrRNA.fq
  • vignette/tmp/WT3AT/rRNA_map.sam
1
hisat2 --version &> {log}; hisat2 -p {config[num_processes]} -N 1 -k 1 --un {output.fq} -x {params.prefix} -S {output.sam} -U {input.fq} &>> {log}
build_indices_rrna 1
  • vignette/index/yeast_rRNA.1.ht2
  • vignette/index/yeast_rRNA.2.ht2
  • vignette/index/yeast_rRNA.3.ht2
  • vignette/index/yeast_rRNA.4.ht2
  • vignette/index/yeast_rRNA.5.ht2
  • vignette/index/yeast_rRNA.6.ht2
  • vignette/index/yeast_rRNA.7.ht2
  • vignette/index/yeast_rRNA.8.ht2
1
hisat2-build --version &> {log}; hisat2-build {input} {params.prefix} &>> {log}
cut_adapters 2
  • vignette/tmp/WTnone/trim.fq
  • vignette/tmp/WT3AT/trim.fq
1
cutadapt --trim-n -O 1 -m 5 -a	{config[adapters]} -o {output} {input} -j 0 &> {log}