def rnaseq(samples):
prep = [
s("prep_samples",
"multi-parallel", [["files"], dd.get_keys("sample_name")],
[cwlout(["files"], "File")],
"bcbio",
programs=["picard"])
]
align = [
s("process_alignment", "multi-parallel",
[["files"], ["reference", "fasta", "base"], ["analysis"],
["rgnames", "pl"], ["rgnames", "sample"], ["rgnames", "pu"],
["rgnames", "lane"], ["rgnames", "rg"], ["rgnames", "lb"],
["reference", "aligner", "indexes"],
["config", "algorithm", "aligner"],
["genome_resources", "rnaseq", "transcripts"],
["config", "algorithm", "quality_format"]], [
cwlout(["work_bam"], "File", [".bai"]),
cwlout(["align_bam"], "File", [".bai"])
], "bcbio-vc", ["aligner", "samtools", "sambamba", "seqtk"],
{"files": 1.5})
]
quantitate = [
s("rnaseq_quantitate",
"multi-parallel", [["files"],
dd.get_keys("work_bam"),
dd.get_keys("gtf_file"),
dd.get_keys("ref_file"),
dd.get_keys("genome_build")], [
cwlout(dd.get_keys("count_file"), "File"),
cwlout(dd.get_keys("sailfish_dir"), "File")
],
"bcbio",
programs=["sailfish"],
disk={"files": 1.5})
]
qc = [
s("pipeline_summary", "multi-parallel",
[["align_bam"], ["analysis"], ["reference", "fasta", "base"],
["config", "algorithm", "qc"]], [
cwlout(["summary", "qc", "samtools"], "File"),
cwlout(["summary", "qc", "fastqc"], "File")
], "bcbio", ["samtools", "fastqc"]),
s("multiqc_summary", "multi-combined",
[["genome_build"], ["summary", "qc", "samtools"],
["summary", "qc", "fastqc"], ["reference", "fasta", "base"],
["config", "algorithm", "coverage_interval"]],
[cwlout(["summary", "multiqc"], ["File", "null"])], "bcbio")
]
steps = prep + align + quantitate + qc
final_outputs = [
dd.get_keys("work_bam"),
dd.get_keys("sailfish_dir"), ["summary", "multiqc"]
]
return steps, final_outputs
def rnaseq(samples):
prep = [s("prep_samples", "multi-parallel",
[["files"],
dd.get_keys("sample_name")],
[cwlout(["files"], "File")],
"bcbio", programs=["picard"])]
align = [s("process_alignment", "multi-parallel",
[["files"], ["reference", "fasta", "base"],
["analysis"],
["rgnames", "pl"], ["rgnames", "sample"], ["rgnames", "pu"],
["rgnames", "lane"], ["rgnames", "rg"], ["rgnames", "lb"],
["reference", "aligner", "indexes"],
["config", "algorithm", "aligner"],
["genome_resources", "rnaseq", "transcripts"],
["config", "algorithm", "quality_format"]],
[cwlout(["work_bam"], "File", [".bai"]),
cwlout(["align_bam"], "File", [".bai"])],
"bcbio-vc", ["aligner", "samtools", "sambamba", "seqtk"],
{"files": 1.5})]
quantitate = [s("rnaseq_quantitate", "multi-parallel",
[["files"],
dd.get_keys("work_bam"),
dd.get_keys("gtf_file"),
dd.get_keys("ref_file"),
dd.get_keys("genome_build")],
[cwlout(dd.get_keys("count_file"), "File"),
cwlout(dd.get_keys("sailfish_dir"), "File")],
"bcbio", programs=["sailfish"],
disk={"files": 1.5})]
qc = [s("pipeline_summary", "multi-parallel",
[["align_bam"], ["analysis"], ["reference", "fasta", "base"],
["config", "algorithm", "qc"]],
[cwlout(["summary", "qc", "samtools"], "File"),
cwlout(["summary", "qc", "fastqc"], "File")],
"bcbio", ["samtools", "fastqc"]),
s("multiqc_summary", "multi-combined",
[["genome_build"], ["summary", "qc", "samtools"], ["summary", "qc", "fastqc"],
["reference", "fasta", "base"], ["config", "algorithm", "coverage_interval"]],
[cwlout(["summary", "multiqc"], ["File", "null"])],
"bcbio")]
steps = prep + align + quantitate + qc
final_outputs = [dd.get_keys("work_bam"), dd.get_keys("sailfish_dir"),
["summary", "multiqc"]]
return steps, final_outputs
def rnaseq(samples):
prep = [s("prepare_sample", "multi-parallel",
[["files"], dd.get_keys("sample_name"),
dd.get_keys("ref_file"), dd.get_keys("genome_build"), dd.get_keys("gtf_file"),
["analysis"],
["rgnames", "pl"], ["rgnames", "pu"], ["rgnames", "lane"], ["rgnames", "rg"], ["rgnames", "lb"],
["reference", "aligner", "indexes"],
["config", "algorithm", "aligner"],
["config", "algorithm", "expression_caller"],
["config", "algorithm", "quality_format"]],
[cwlout("prep_rec", "record")],
"bcbio-rnaseq", programs=["picard", "samtools", "pysam>=0.13.0"]),
s("trim_sample", "multi-parallel",
[["prep_rec"]],
[cwlout("trim_rec", "record")],
"bcbio-rnaseq", programs=["atropos;env=python3"])]
align = [s("process_alignment", "multi-parallel",
[["trim_rec"]],
[cwlout(["work_bam"], "File", [".bai"])],
"bcbio-rnaseq", ["star", "hisat2", "tophat", "samtools",
"sambamba", "seqtk"],
{"files": 1.5})]
quantitate = [s("rnaseq_quantitate", "multi-parallel",
[["trim_rec"], ["work_bam"]],
[cwlout(dd.get_keys("count_file"), "File"),
cwlout(["quant", "tsv"], "File"),
cwlout(["quant", "hdf5"], "File")],
"bcbio-rnaseq", programs=["sailfish", "salmon", "kallisto>=0.43.1", "subread", "gffread",
"r=3.4.1", "r-wasabi"],
disk={"files": 0.5})]
qc = [s("qc_to_rec", "multi-combined",
[["work_bam"], ["analysis"], ["reference", "fasta", "base"], dd.get_keys("gtf_file"),
["genome_build"], ["config", "algorithm", "coverage_interval"],
["config", "algorithm", "tools_on"], ["config", "algorithm", "tools_off"],
["config", "algorithm", "qc"]],
[cwlout("qc_rec", "record")],
"bcbio-rnaseq", disk={"files": 1.5}, cores=1, no_files=True),
s("pipeline_summary", "multi-parallel",
[["qc_rec"]],
[cwlout("qcout_rec", "record",
fields=[cwlout(["summary", "qc"], ["File", "null"]),
cwlout(["summary", "metrics"], ["string", "null"]),
cwlout("inherit")])],
"bcbio-rnaseq", ["bedtools", "fastqc", "goleft", "hts-nim-tools", "mosdepth",
"picard", "pythonpy", "qsignature", "qualimap",
"sambamba", "samtools"]),
s("multiqc_summary", "multi-combined",
[["qcout_rec"]],
[cwlout(["summary", "multiqc"], ["File", "null"])],
"bcbio-rnaseq", ["multiqc", "multiqc-bcbio"])]
steps = prep + align + quantitate + qc
final_outputs = [dd.get_keys("work_bam"), ["quant", "tsv"], ["summary", "multiqc"]]
return steps, final_outputs
def fastrnaseq():
prep = [s("prep_samples", "multi-parallel",
[["files"],
dd.get_keys("sample_name")],
[cwlout(["files"], "File")],
programs=["picard"])]
quant = [s("run_salmon_reads", "multi-parallel",
[["files"],
dd.get_keys("sample_name"),
dd.get_keys("gtf_file"),
dd.get_keys("ref_file"),
dd.get_keys("genome_build")],
[cwlout(dd.get_keys("sailfish_dir"), "File")],
programs=["salmon"],
disk={"files": 1.5})]
steps = quant
final_outputs = [dd.get_keys('sailfish_dir')]
return steps, final_outputs
def fastrnaseq(samples):
prep = [s("prep_samples", "multi-parallel",
[["files"],
dd.get_keys("sample_name")],
[cwlout(["files"], "File")],
"bcbio", programs=["picard"])]
quant = [s("run_salmon_reads", "multi-parallel",
[["files"],
dd.get_keys("sample_name"),
dd.get_keys("gtf_file"),
dd.get_keys("ref_file"),
dd.get_keys("genome_build")],
[cwlout(dd.get_keys("sailfish_dir"), "File")],
"bcbio", programs=["salmon"],
disk={"files": 1.5})]
steps = quant
final_outputs = [dd.get_keys('sailfish_dir')]
return steps, final_outputs
def rnaseq(samples):
checkpoints = _rnaseq_checkpoints(samples)
prep = [
s("prepare_sample",
"multi-parallel",
[["files"],
dd.get_keys("sample_name"),
dd.get_keys("ref_file"),
dd.get_keys("genome_build"),
dd.get_keys("gtf_file"), ["analysis"], ["rgnames", "pl"],
["rgnames", "pu"], ["rgnames", "lane"], ["rgnames", "rg"],
["rgnames", "lb"], ["reference", "aligner", "indexes"],
["config", "algorithm", "aligner"],
["config", "algorithm", "expression_caller"],
["config", "algorithm", "fusion_caller"],
["config", "algorithm", "quality_format"]],
[cwlout("prep_rec", "record")],
"bcbio-rnaseq",
programs=["picard", "samtools", "pysam>=0.13.0"]),
s("trim_sample",
"multi-parallel", [["prep_rec"]], [cwlout("trim_rec", "record")],
"bcbio-rnaseq",
programs=["atropos;env=python3"])
]
align = [
s("process_alignment", "multi-parallel", [["trim_rec"]],
[cwlout(["align_bam"], "File", [".bai"])], "bcbio-rnaseq", [
"star", "hisat2", "tophat;env=python2", "samtools", "sambamba",
"seqtk"
], {"files": 1.5})
]
if checkpoints.get("vc"):
pp_align, pp_align_out = _postprocess_alignment(checkpoints)
else:
pp_align, pp_align_out = [], []
quantitate = [
s("rnaseq_quantitate",
"multi-parallel", [["trim_rec"], ["align_bam"]], [
cwlout(dd.get_keys("count_file"), "File"),
cwlout(["quant", "tsv"], "File"),
cwlout(["quant", "hdf5"], "File"),
cwlout(["quant", "fusion"], "File")
],
"bcbio-rnaseq",
programs=[
"sailfish", "salmon", "kallisto>=0.43.1", "subread", "gffread",
"r=3.4.1", "r-base=3.4.1=h4fe35fd_8", "xorg-libxt", "r-wasabi"
],
disk={"files": 0.5})
]
qc = [
s("qc_to_rec",
"multi-combined",
[["align_bam"], ["analysis"], ["reference", "fasta", "base"],
dd.get_keys("gtf_file"), ["genome_build"],
["config", "algorithm", "coverage_interval"],
["config", "algorithm", "tools_on"],
["config", "algorithm", "tools_off"], ["config", "algorithm", "qc"]
], [cwlout("qc_rec", "record")],
"bcbio-rnaseq",
disk={"files": 1.5},
cores=1,
no_files=True),
s("pipeline_summary", "multi-parallel", [["qc_rec"]], [
cwlout("qcout_rec",
"record",
fields=[
cwlout(["summary", "qc"], ["File", "null"]),
cwlout(["summary", "metrics"], ["string", "null"]),
cwlout("inherit")
])
], "bcbio-rnaseq", [
"bedtools", "fastqc=0.11.7=5", "goleft", "hts-nim-tools",
"mosdepth", "picard", "pythonpy", "qsignature", "qualimap",
"sambamba", "samtools"
]),
s("multiqc_summary", "multi-combined", [["qcout_rec"]],
[cwlout(["summary", "multiqc"], ["File", "null"])], "bcbio-rnaseq",
["multiqc", "multiqc-bcbio"])
]
vc, vc_out = _variant_vc(checkpoints)
fusion = [
s("detect_fusions", "multi-parallel",
[["quant", "fusion"], ["quant", "hdf5"], ["trim_rec"]], [
cwlout(["fusion", "fasta"], "File"),
cwlout(["fusion", "json"], "File")
], "bcbio-rnaseq", ["pizzly"])
]
steps = prep + align + pp_align + quantitate + qc + vc + fusion
final_outputs = [["rgnames", "sample"], dd.get_keys("align_bam"), ["quant", "tsv"], ["summary", "multiqc"]] + \
vc_out + pp_align_out
return steps, final_outputs
def rnaseq(samples):
checkpoints = _rnaseq_checkpoints(samples)
prep = [s("prepare_sample", "multi-parallel",
[["files"], dd.get_keys("sample_name"),
dd.get_keys("ref_file"), dd.get_keys("genome_build"), dd.get_keys("gtf_file"),
["analysis"],
["rgnames", "pl"], ["rgnames", "pu"], ["rgnames", "lane"],
["rgnames", "rg"], ["rgnames", "lb"],
["reference", "aligner", "indexes"],
["config", "algorithm", "aligner"],
["config", "algorithm", "expression_caller"],
["config", "algorithm", "fusion_caller"],
["config", "algorithm", "quality_format"]],
[cwlout("prep_rec", "record")],
"bcbio-rnaseq", programs=["picard", "samtools", "pysam>=0.13.0"]),
s("trim_sample", "multi-parallel",
[["prep_rec"]],
[cwlout("trim_rec", "record")],
"bcbio-rnaseq", programs=["atropos;env=python3"])]
align = [s("process_alignment", "multi-parallel",
[["trim_rec"]],
[cwlout(["align_bam"], "File", [".bai"])],
"bcbio-rnaseq", ["star", "hisat2", "tophat;env=python2", "samtools",
"sambamba", "seqtk"],
{"files": 1.5})]
if checkpoints.get("vc"):
pp_align, pp_align_out = _postprocess_alignment(checkpoints)
else:
pp_align, pp_align_out = [], []
quantitate = [s("rnaseq_quantitate", "multi-parallel",
[["trim_rec"], ["align_bam"]],
[cwlout(dd.get_keys("count_file"), "File"),
cwlout(["quant", "tsv"], "File"),
cwlout(["quant", "hdf5"], "File"),
cwlout(["quant", "fusion"], "File")],
"bcbio-rnaseq", programs=["sailfish", "salmon", "kallisto>=0.43.1", "subread", "gffread",
"r=3.4.1", "r-base=3.4.1=h4fe35fd_8", "xorg-libxt", "r-wasabi"],
disk={"files": 0.5})]
qc = [s("qc_to_rec", "multi-combined",
[["align_bam"], ["analysis"], ["reference", "fasta", "base"], dd.get_keys("gtf_file"),
["genome_build"], ["config", "algorithm", "coverage_interval"],
["config", "algorithm", "tools_on"], ["config", "algorithm", "tools_off"],
["config", "algorithm", "qc"]],
[cwlout("qc_rec", "record")],
"bcbio-rnaseq", disk={"files": 1.5}, cores=1, no_files=True),
s("pipeline_summary", "multi-parallel",
[["qc_rec"]],
[cwlout("qcout_rec", "record",
fields=[cwlout(["summary", "qc"], ["File", "null"]),
cwlout(["summary", "metrics"], ["string", "null"]),
cwlout("inherit")])],
"bcbio-rnaseq", ["bedtools", "fastqc=0.11.7=5", "goleft", "hts-nim-tools", "mosdepth",
"picard", "pythonpy", "qsignature", "qualimap",
"sambamba", "samtools"]),
s("multiqc_summary", "multi-combined",
[["qcout_rec"]],
[cwlout(["summary", "multiqc"], ["File", "null"])],
"bcbio-rnaseq", ["multiqc", "multiqc-bcbio"])]
vc, vc_out = _variant_vc(checkpoints)
fusion = [s("detect_fusions", "multi-parallel",
[["quant", "fusion"], ["quant", "hdf5"], ["trim_rec"]],
[cwlout(["fusion", "fasta"], "File"),
cwlout(["fusion", "json"], "File")],
"bcbio-rnaseq", ["pizzly"])]
steps = prep + align + pp_align + quantitate + qc + vc + fusion
final_outputs = [["rgnames", "sample"], dd.get_keys("align_bam"), ["quant", "tsv"], ["summary", "multiqc"]] + \
vc_out + pp_align_out
return steps, final_outputs
