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Commit 1f97d055 authored by CJHerrmann's avatar CJHerrmann
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typos, formatting

parent 019a1037
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1 merge request!83feat: enable user to configure CLI params per rule
Pipeline #12367 passed
Stage: test
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Snakefile
+ 186
− 23
View file @ 1f97d055
......@@ -210,7 +210,13 @@ rule fastqc:
"{mate}"))
params:
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--outdir',))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--outdir',
)
)
threads: 2
......@@ -282,7 +288,18 @@ rule create_index_star:
"{index_size}",
"STAR_index/STAR_"),
sjdbOverhang = "{index_size}",
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--runMode','--sjdbOverhang', '--genomeDir', '--genomeFastaFiles', '--outFileNamePrefix', '--sjdbGTFfile'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--runMode',
'--sjdbOverhang',
'--genomeDir',
'--genomeFastaFiles',
'--outFileNamePrefix',
'--sjdbGTFfile',
)
)
singularity:
"docker://zavolab/star:2.7.3a-slim"
......@@ -336,7 +353,14 @@ rule extract_transcriptome:
"transcriptome.fa"))
params:
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('-w', '-g'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-w',
'-g',
)
)
log:
stderr = os.path.join(
......@@ -426,7 +450,16 @@ rule create_index_salmon:
params:
kmerLen = "{kmer}",
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--transcripts','--decoys', '--index', '--kmerLen'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--transcripts',
'--decoys',
'--index',
'--kmerLen',
)
)
singularity:
"docker://zavolab/salmon:1.1.0-slim"
......@@ -474,7 +507,13 @@ rule create_index_kallisto:
output_dir = os.path.join(
config['kallisto_indexes'],
"{organism}"),
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('-i',))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-i',
)
)
singularity:
"docker://zavolab/kallisto:0.46.1-slim"
......@@ -512,7 +551,14 @@ rule extract_transcripts_as_bed12:
"full_transcripts_protein_coding.bed"))
params:
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--gtf', '--bed12'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--gtf',
'--bed12',
)
)
singularity:
"docker://zavolab/zgtf:0.1"
......@@ -556,7 +602,11 @@ rule index_genomic_alignment_samtools:
"{sample}.{seqmode}.Aligned.sortedByCoord.out.bam.bai")
params:
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=())
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=()
)
singularity:
"docker://zavolab/samtools:1.10-slim"
......@@ -628,7 +678,15 @@ rule calculate_TIN_scores:
params:
sample = "{sample}",
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('-i', '-r', '--names'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-i',
'-r',
'--names',
)
)
log:
stderr = os.path.join(
......@@ -697,7 +755,18 @@ rule salmon_quantmerge_genes:
"{sample}",
sample=pd.unique(samples_table.index.values)),
salmon_merge_on = "{salmon_merge_on}",
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--quants', '--genes', '--transcripts', '--names', '--column', '--output'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--quants',
'--genes',
'--transcripts',
'--names',
'--column',
'--output',
)
)
log:
stderr = os.path.join(
......@@ -765,12 +834,22 @@ rule salmon_quantmerge_transcripts:
search_id='index',
search_value=i)
for i in pd.unique(samples_table.index.values)]),
sample_name_list = expand(
"{sample}",
sample=pd.unique(samples_table.index.values)),
salmon_merge_on = "{salmon_merge_on}",
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--quants', '--genes', '--transcripts', '--names', '--column', '--output'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--quants',
'--genes',
'--transcripts',
'--names',
'--column',
'--output',
)
)
log:
stderr = os.path.join(
......@@ -842,7 +921,17 @@ rule kallisto_merge_genes:
sample_name_list = ','.join(expand(
"{sample}",
sample=pd.unique(samples_table.index.values))),
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--input', '--names', '--txOut', '--anno', '--output'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--input',
'--names',
'--txOut',
'--anno',
'--output',
)
)
log:
stderr = os.path.join(
......@@ -914,7 +1003,16 @@ rule kallisto_merge_transcripts:
sample_name_list = ','.join(expand(
"{sample}",
sample=pd.unique(samples_table.index.values))),
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--input', '--names', '--txOut', '--output'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--input',
'--names',
'--txOut',
'--output',
)
)
log:
stderr = os.path.join(
......@@ -954,7 +1052,14 @@ rule pca_salmon:
"pca_salmon_{molecule}"))
params:
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--tpm', '--out'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--tpm',
'--out',
)
)
log:
stderr = os.path.join(
......@@ -993,7 +1098,14 @@ rule pca_kallisto:
"pca_kallisto_{molecule}"))
params:
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--tpm', '--out'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--tpm',
'--out',
)
)
log:
stderr = os.path.join(
......@@ -1084,7 +1196,16 @@ rule star_rpm:
os.path.join(
os.path.dirname(output.str1),
str(wildcards.sample) + "_"),
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--runMode', '--inputBAMfile', '--outWigType', '--outFileNamePrefix'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--runMode',
'--inputBAMfile',
'--outWigType',
'--outFileNamePrefix',
)
)
singularity:
"docker://zavolab/star:2.7.3a-slim"
......@@ -1194,7 +1315,6 @@ rule generate_alfa_index:
'gtf',
search_id='organism',
search_value=wildcards.organism)),
chr_len = os.path.join(
config["star_indexes"],
"{organism}",
......@@ -1220,7 +1340,16 @@ rule generate_alfa_index:
genome_index = "sorted_genes",
out_dir = lambda wildcards, output:
os.path.dirname(output.index_stranded),
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('-a', '-g', '--chr_len', '-o'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-a',
'-g',
'--chr_len',
'-o',
)
)
threads: 4
......@@ -1317,7 +1446,15 @@ rule alfa_qc:
'alfa_directionality',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('-g', '--bedgraph', '-s'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-g',
'--bedgraph',
'-s',
)
)
singularity:
"docker://zavolab/alfa:1.1.1-slim"
......@@ -1360,7 +1497,16 @@ rule prepare_multiqc_config:
logo_path = config['report_logo'],
multiqc_intro_text = config['report_description'],
url = config['report_url'],
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--config', '--intro-text', '--custom-logo', '--url'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--config',
'--intro-text',
'--custom-logo',
'--url',
)
)
log:
stderr = os.path.join(
......@@ -1466,7 +1612,14 @@ rule multiqc_report:
results_dir = os.path.join(
config["output_dir"]),
log_dir = config["log_dir"],
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('--outdir', '--config'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--outdir',
'--config',
)
)
log:
stderr = os.path.join(
......@@ -1512,7 +1665,13 @@ rule sort_bed_4_big:
"{sample}_{unique}_{strand}.sorted.bg"))
params:
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=('-i', ))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-i',
)
)
singularity:
"docker://cjh4zavolab/bedtools:2.27"
......@@ -1568,7 +1727,11 @@ rule prepare_bigWig:
"{sample}_{unique}_{strand}.bw")
params:
additional_params = parse_rule_config(rule_config, current_rule=current_rule, immutable=())
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=()
)
singularity:
"docker://zavolab/bedgraphtobigwig:4-slim"
......
pipeline_documentation.md
+ 2
− 2
View file @ 1f97d055
......@@ -104,7 +104,7 @@ sample | Descriptive sample name | `str`
seqmode | Required for various steps of the workflow. One of `pe` (for paired-end libraries) or `se` (for single-end libraries). | `str`
fq1 | Path of library file in `.fastq.gz` format (or mate 1 read file for paired-end libraries) | `str`
index_size | Required for [STAR](#third-party-software-used). Ideally the maximum read length minus 1 (`max(ReadLength)-1`). Values lower than maximum read length may result in lower mapping accuracy, while higher values may result in longer processing times. | `int`
kmer | Required for [Salmon](#third-party-software-used). Default value of 31 usually works fine for reads of 75 bp or longer. Consider using lower values of poor mapping is observed. | `int`
kmer | Required for [Salmon](#third-party-software-used). Default value of 31 usually works fine for reads of 75 bp or longer. Consider using lower values if poor mapping is observed. | `int`
fq2 | Path of mate 2 read file in `.fastq.gz` format. Value ignored for for single-end libraries. | `str`
fq1_3p | Required for [Cutadapt](#third-party-software-used). 3' adapter of mate 1. Use value such as `XXXXXXXXXXXXXXX` if no adapter present or if no trimming is desired. | `str`
fq1_5p | Required for [Cutadapt](#third-party-software-used). 5' adapter of mate 1. Use value such as `XXXXXXXXXXXXXXX` if no adapter present or if no trimming is desired. | `str`
......@@ -157,7 +157,7 @@ Create index for [**STAR**](#third-party-software-used) short read aligner.
- Gene annotation file (`.gtf`)
- **Parameters**
- **samples.tsv**
- `--sjdbOverhang`: maximum read length - 1; lower values may reduce accuracy,higher values may increase STAR runtime; specify in sample table column `index_size`
- `--sjdbOverhang`: maximum read length - 1; lower values may reduce accuracy, higher values may increase STAR runtime; specify in sample table column `index_size`
- **Output**
- STAR index; used in [**map_genome_star**](#map_genome_star)
- Index includes files:
......
workflow/rules/paired_end.snakefile.smk
+ 74
− 10
View file @ 1f97d055
......@@ -39,7 +39,18 @@ rule pe_remove_adapters_cutadapt:
get_sample('fq2_3p', search_id='index', search_value=wildcards.sample),
adapter_5_mate2 = lambda wildcards:
get_sample('fq2_5p', search_id='index', search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('-a', '-A', '-g', '-G', '-o', '-p'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-a',
'-A',
'-g',
'-G',
'-o',
'-p',
)
)
singularity:
"docker://zavolab/cutadapt:1.16-slim"
......@@ -123,7 +134,18 @@ rule pe_remove_polya_cutadapt:
'fq2_polya_5p',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('-a', '-A', '-g', '-G', '-o', '-p'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-a',
'-A',
'-g',
'-G',
'-o',
'-p',
)
)
singularity:
"docker://zavolab/cutadapt:1.16-slim"
......@@ -174,8 +196,8 @@ rule pe_map_genome_star:
'index_size',
search_id='index',
search_value=wildcards.sample),
"STAR_index",
"chrNameLength.txt"),
"STAR_index",
"chrNameLength.txt"),
reads1 = os.path.join(
config["output_dir"],
"samples",
......@@ -216,7 +238,7 @@ rule pe_map_genome_star:
'index_size',
search_id='index',
search_value=wildcards.sample),
"STAR_index")),
"STAR_index")),
outFileNamePrefix = os.path.join(
config["output_dir"],
"samples",
......@@ -238,7 +260,23 @@ rule pe_map_genome_star:
'pass_mode',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('--twopassMode', '--genomeDir', '--readFilesIn', '--readFilesCommand', '--outFilterMultimapNmax', '--outFileNamePrefix', '--outSAMattributes', '--outStd', '--outSAMtype', '--outSAMattrRGline', '--alignEndsType'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--twopassMode',
'--genomeDir',
'--readFilesIn',
'--readFilesCommand',
'--outFilterMultimapNmax',
'--outFileNamePrefix',
'--outSAMattributes',
'--outStd',
'--outSAMtype',
'--outSAMattrRGline',
'--alignEndsType',
)
)
singularity:
"docker://zavolab/star:2.7.3a-slim"
......@@ -303,7 +341,7 @@ rule pe_quantification_salmon:
'kmer',
search_id='index',
search_value=wildcards.sample),
"salmon.idx")
"salmon.idx")
output:
gn_estimates = os.path.join(
......@@ -346,7 +384,20 @@ rule pe_quantification_salmon:
'libtype',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('--libType', '--fldMean', '--fldSD', '--index', '--geneMap', '-1', '-2', '-o'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--libType',
'--fldMean',
'--fldSD',
'--index',
'--geneMap',
'-1',
'-2',
'-o',
)
)
log:
stderr = os.path.join(
......@@ -401,7 +452,7 @@ rule pe_genome_quantification_kallisto:
'organism',
search_id='index',
search_value=wildcards.sample),
"kallisto.idx")
"kallisto.idx")
output:
pseudoalignment = os.path.join(
......@@ -430,7 +481,20 @@ rule pe_genome_quantification_kallisto:
'kallisto_directionality',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('--single', '-i', '-o', '-l', '-s', '--pseudobam', '--fr-stranded', '--rf-stranded'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--single',
'-i',
'-o',
'-l',
'-s',
'--pseudobam',
'--fr-stranded',
'--rf-stranded',
)
)
singularity:
......
workflow/rules/single_end.snakefile.smk
+ 68
− 5
View file @ 1f97d055
......@@ -29,7 +29,18 @@ rule remove_adapters_cutadapt:
'fq1_5p',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('-a', '-A', '-g', '-G', '-o', '-p'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-a',
'-A',
'-g',
'-G',
'-o',
'-p',
)
)
singularity:
"docker://zavolab/cutadapt:1.16-slim"
......@@ -88,7 +99,18 @@ rule remove_polya_cutadapt:
'fq1_polya_5p',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('-a', '-A', '-g', '-G', '-o', '-p'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'-a',
'-A',
'-g',
'-G',
'-o',
'-p',
)
)
singularity:
"docker://zavolab/cutadapt:1.16-slim"
......@@ -182,7 +204,23 @@ rule map_genome_star:
'pass_mode',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('--twopassMode', '--genomeDir', '--readFilesIn', '--readFilesCommand', '--outFilterMultimapNmax', '--outFileNamePrefix', '--outSAMattributes', '--outStd', '--outSAMtype', '--outSAMattrRGline', '--alignEndsType'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--twopassMode',
'--genomeDir',
'--readFilesIn',
'--readFilesCommand',
'--outFilterMultimapNmax',
'--outFileNamePrefix',
'--outSAMattributes',
'--outStd',
'--outSAMtype',
'--outSAMattrRGline',
'--alignEndsType',
)
)
singularity:
"docker://zavolab/star:2.7.3a-slim"
......@@ -295,7 +333,19 @@ rule quantification_salmon:
'sd',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('--libType', '--fldMean', '--fldSD', '--index', '--geneMap', '--unmatedReads', '-o'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--libType',
'--fldMean',
'--fldSD',
'--index',
'--geneMap',
'--unmatedReads',
'-o',
)
)
log:
stderr = os.path.join(
config["log_dir"],
......@@ -384,7 +434,20 @@ rule genome_quantification_kallisto:
'kallisto_directionality',
search_id='index',
search_value=wildcards.sample),
additional_params = parse_rule_config(rule_config,current_rule=current_rule, immutable=('--single', '-i', '-o', '-l', '-s', '--pseudobam', '--fr-stranded', '--rf-stranded'))
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
immutable=(
'--single',
'-i',
'-o',
'-l',
'-s',
'--pseudobam',
'--fr-stranded',
'--rf-stranded',
)
)
threads: 8
......
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