Remove SRST2 from wdl, dockerfile, dag

chanzuckerberg · May 7, 2024 · d95d3c6 · d95d3c6
1 parent 4ccee1a
commit d95d3c6
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diff --git a/lib/idseq-dag/idseq_dag/steps/run_srst2.py b/lib/idseq-dag/idseq_dag/steps/run_srst2.py
diff --git a/workflows/short-read-mngs/Dockerfile b/workflows/short-read-mngs/Dockerfile
@@ -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

diff --git a/workflows/short-read-mngs/experimental.wdl b/workflows/short-read-mngs/experimental.wdl
@@ -113,44 +113,7 @@ task GenerateAlignmentViz {
   }
   runtime {
     docker: docker_image_id
-  }
-}
-
-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 {
@@ -287,16 +250,6 @@ 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,
@@ -340,13 +293,6 @@ 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