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Remove SRST2 from workflows #354

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May 8, 2024
Merged

Remove SRST2 from workflows #354

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d95d3c6
Remove SRST2 from wdl, dockerfile, dag
lvreynoso May 7, 2024
e69578c
Lint
lvreynoso May 7, 2024
64ba2c3
Test release
lvreynoso May 8, 2024
6c3fbad
Revert release
lvreynoso May 8, 2024
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302 changes: 0 additions & 302 deletions lib/idseq-dag/idseq_dag/steps/run_srst2.py
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5 changes: 0 additions & 5 deletions workflows/short-read-mngs/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -119,11 +119,6 @@ RUN curl -Ls https://github.com/chanzuckerberg/s3parcp/releases/download/v0.2.0-
# FIXME: check if use of pandas, pysam is necessary
RUN pip3 install pysam==0.14.1 pandas==1.1.5

# Workaround for srst2 refusing to work with upstream bowtie2 and samtools
# FIXME: replace srst2 with a more appropriate tool
RUN apt-get -q install -y srst2
RUN sed -i '/Incorrect version/ s/\w.*/return "1.7"/' /usr/bin/srst2

# Picard for average fragment size https://github.com/broadinstitute/picard
# r-base is a dependency of collecting input size metrics https://github.com/bioconda/bioconda-recipes/pull/16398
RUN apt-get install -y r-base
Expand Down
53 changes: 0 additions & 53 deletions workflows/short-read-mngs/experimental.wdl
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Expand Up @@ -116,42 +116,6 @@ task GenerateAlignmentViz {
}
}

task RunSRST2 {
input {
String docker_image_id
String s3_wd_uri
Array[File] fastqs
String file_ext
File resist_genome_db
File resist_genome_bed
}
command<<<
set -euxo pipefail
idseq-dag-run-step --workflow-name experimental \
--step-module idseq_dag.steps.run_srst2 \
--step-class PipelineStepRunSRST2 \
--step-name srst2_out \
--input-files '[["~{sep='","' fastqs}"]]' \
--output-files '["out.log", "out__genes__ARGannot_r2__results.txt", "out__fullgenes__ARGannot_r2__results.txt", "amr_processed_results.csv", "amr_summary_results.csv", "output__.ARGannot_r2.sorted.bam"]' \
--output-dir-s3 '~{s3_wd_uri}' \
--additional-files '{"resist_gene_db": "~{resist_genome_db}", "resist_genome_bed": "~{resist_genome_bed}"}' \
--additional-attributes '{"min_cov": 0, "n_threads": 16, "file_ext": "~{file_ext}"}'
>>>
output {
String step_description_md = read_string("srst2_out.description.md")
File out_log = "out.log"
File out__genes__ARGannot_r2__results_txt = "out__genes__ARGannot_r2__results.txt"
File out__fullgenes__ARGannot_r2__results_txt = "out__fullgenes__ARGannot_r2__results.txt"
File amr_processed_results_csv = "amr_processed_results.csv"
File amr_summary_results_csv = "amr_summary_results.csv"
File output___ARGannot_r2_sorted_bam = "output__.ARGannot_r2.sorted.bam"
File? output_read_count = "srst2_out.count"
}
runtime {
docker: docker_image_id
}
}

task GenerateCoverageViz {
input {
String docker_image_id
Expand Down Expand Up @@ -287,16 +251,6 @@ workflow czid_experimental {
nt_loc_db = nt_loc_db
}

call RunSRST2 {
input:
docker_image_id = docker_image_id,
s3_wd_uri = s3_wd_uri,
fastqs = select_all([fastqs_0, fastqs_1]),
file_ext = file_ext,
resist_genome_db = resist_genome_db,
resist_genome_bed = resist_genome_bed
}

call GenerateCoverageViz {
input:
docker_image_id = docker_image_id,
Expand Down Expand Up @@ -340,13 +294,6 @@ workflow czid_experimental {
File? taxid_locator_out_count = GenerateTaxidLocator.output_read_count
File alignment_viz_out_align_viz_summary = GenerateAlignmentViz.align_viz_summary
File? alignment_viz_out_count = GenerateAlignmentViz.output_read_count
File srst2_out_out_log = RunSRST2.out_log
File srst2_out_out__genes__ARGannot_r2__results_txt = RunSRST2.out__genes__ARGannot_r2__results_txt
File srst2_out_out__fullgenes__ARGannot_r2__results_txt = RunSRST2.out__fullgenes__ARGannot_r2__results_txt
File srst2_out_amr_processed_results_csv = RunSRST2.amr_processed_results_csv
File srst2_out_amr_summary_results_csv = RunSRST2.amr_summary_results_csv
File srst2_out_output___ARGannot_r2_sorted_bam = RunSRST2.output___ARGannot_r2_sorted_bam
File? srst2_out_count = RunSRST2.output_read_count
File coverage_viz_out_coverage_viz_summary_json = GenerateCoverageViz.coverage_viz_summary_json
File? coverage_viz_out_count = GenerateCoverageViz.output_read_count
File nonhost_fastq_out_nonhost_R1_fastq = NonhostFastq.nonhost_R1_fastq
Expand Down
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