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update pipeline
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@RAHenriksen
RAHenriksen committed Dec 2, 2024
1 parent f656a9a commit 22dac9b
Showing 1 changed file with 40 additions and 14 deletions.
54 changes: 40 additions & 14 deletions bifrost_sp_cdiff/pipeline.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -125,11 +125,39 @@ rule run_cdifftyping:
update = "no",
output:
folder = directory(rules.setup.params.folder + "/cdiff_analysis"),
_R1 = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/cdifffiltered_R1.fastq",
_R2 = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/cdifffiltered_R2.fastq",
_txt = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}_assessment_report.txt",
_bam = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.bam",
_bai = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.bam.bai",
_cdtA = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}_cdtA.info",
_cdtB = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}_cdtB.info",
_tcdA = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}_tcdA.info",
_tcdB = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}_tcdB.info",
_tcdC = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}_tcdC.info",
_coverage = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.coverage",
_counts = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.coverage.sample_cumulative_coverage_counts",
_proportions = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.coverage.sample_cumulative_coverage_proportions",
_interval_statistics = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.coverage.sample_interval_statistics",
_interval_summary = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.coverage.sample_interval_summary",
_sample_statistics = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.coverage.sample_statistics",
_sample_summary = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.coverage.sample_summary",
_indel_vcf = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.indel.vcf",
_indel_vcf_idx = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.indel.vcf.idx",
_sam = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.sam",
_snp_indel_vcf = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.snp_indel.vcf",
_snp_indel_vcf_idx = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.snp_indel.vcf.idx",
_snp_vcf = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.snp.vcf",
_snp_vcf_idx = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}.snp.vcf.idx",
_TRST_fasta = f"{rules.setup.params.folder}/cdiff_analysis/{sample_id}/sp_cdiff_fbi/{sample_id}._TRST.fasta",
shell:
"""
echo {rules.run_ecolityping.input.assembly}
echo /home/people/rashen/bifrost_sp_cdiff/bifrost_sp_cdiff/cdiff_fbi/cdifftyping.sh -i {params.sample_id} -R1 {input.reads[0]} -R2 {input.reads[1]} -c {input.assembly} -o {output.folder} -db {input.db} -update {params.update}
#echo {rules.run_ecolityping.input.assembly}
# Type
bash {resources_dir}/bifrost_sp_cdiff/cdiff_fbi/cdifftyping.sh -i {params.sample_id} -R1 {input.reads[0]} -R2 {input.reads[1]} -c {input.assembly} -o {output.folder} -db {input.db} -update {params.update} 1> {log.out_file} 2> {log.err_file}
#bash {resources_dir}/bifrost_sp_cdiff/cdiff_fbi/cdifftyping.sh -i {params.sample_id} -R1 {input.reads[0]} -R2 {input.reads[1]} -c {input.assembly} -o {output.folder} -db {input.db} -update {params.update} 1> {log.out_file} 2> {log.err_file}
bash /home/people/rashen/bifrost_sp_cdiff/bifrost_sp_cdiff/cdiff_fbi/cdifftyping.sh -i {params.sample_id} -R1 {input.reads[0]} -R2 {input.reads[1]} -c {input.assembly} -o {output.folder} -db {input.db} -update {params.update} 1> {log.out_file} 2> {log.err_file}
#bash /home/people/rashen/bifrost_sp_cdiff/bifrost_sp_cdiff/cdiff_fbi/cdifftyping.sh -i testrun_ec___24000006_MW-ESCEC -R1 /home/projects/fvst_ssi_dtu/data/dev/output/ssi/2024/testrun_ec/samples/24000006-MW-ESCEC-run999_S1_L001_R1_001.fastq.gz -R2 /home/projects/fvst_ssi_dtu/data/dev/output/ssi/2024/testrun_ec/samples/24000006-MW-ESCEC-run999_S1_L001_R2_001.fastq.gz -o sp_cdiff -db /home/projects/fvst_ssi_dtu/apps/sofi_bifrost_dev/scripts/bifrost/components/bifrost_sp_cdiff/bifrost_sp_cdiff/cdiff_fbi/db -c assemblatron__v2.3.3/testrun_ec___24000006_MW-ESCEC.fasta -update no
"""

rule_name = "run_postcdifftyping"
Expand All @@ -143,15 +171,16 @@ rule run_postcdifftyping:
f"{component['name']}/benchmarks/{rule_name}.benchmark",
input: # files
rules.check_requirements.output.check_file,
folder = rules.run_cdifftyping.output.folder
params: # values
sample_id = rules.run_cdifftyping.params.sample_id
folder = rules.run_cdifftyping.output.folder,
output:
_file = f"{folder}/{sample_id}.json"
_file = f"{rules.run_cdifftyping.output.folder}/{rules.run_cdifftyping.params.sample_id}/{rules.run_cdifftyping.params.sample_id}.json",
_csv = f"{rules.run_cdifftyping.output.folder}/{rules.run_cdifftyping.params.sample_id}/{rules.run_cdifftyping.params.sample_id}.csv",
shell:
"""
# Process
bash {resources_dir}/bifrost_sp_cdiff/cdiff_fbi/postcdifftyping.sh -i {params.sample_id} -d {input.folder} 1> {log.out_file} 2> {log.err_file}"
#bash {resources_dir}/bifrost_sp_cdiff/cdiff_fbi/postcdifftyping.sh -i {params.sample_id} -d {input.folder} 1> {log.out_file} 2> {log.err_file}"
bash /home/people/rashen/bifrost_sp_cdiff/bifrost_sp_cdiff/cdiff_fbi/postcdifftyping.sh -i {params.sample_id} -d {input.folder} 1> {log.out_file} 2> {log.err_file}
#bash /home/people/rashen/bifrost_sp_cdiff/bifrost_sp_cdiff/cdiff_fbi/postcdifftyping.sh -i testrun_ec___24000006_MW-ESCEC -d {input.folder} -stbit "STNA;NA:NA"
"""


Expand Down Expand Up @@ -188,16 +217,13 @@ rule datadump:
benchmark:
f"{component['name']}/benchmarks/{rule_name}.benchmark"
input:
#* Dynamic section: start ******************************************************************
# TODO
#dtartrate = rules.run_dtartrate.output._file, # Needs to be output of final rule
cdiff_analysis_output_file = run_postcdifftyping.output._file
#subspecies = rules.run_subspecies.output._file # Needs to be output of final rule
#* Dynamic section: end ********************************************************************
cdiff_analysis_output_file = rules.run_postcdifftyping.output._file,
cdiff_analysis_output_csv = rules.run_postcdifftyping.output._csv,
output:
complete = rules.all.input
params:
samplecomponent_ref_json = samplecomponent.to_reference().json
script:
os.path.join(os.path.dirname(workflow.snakefile), "datadump.py")
#f"{resources_dir}/bifrost_sp_cdiff/datadump.py"
f"/home/people/rashen/bifrost_sp_cdiff/bifrost_sp_cdiff/datadump.py"
#- Templated section: end --------------------------------------------------------------------------

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