Merge branch 'resfinder-error' into 'dev'

fail message in report See merge request epi2melabs/workflows/wf-bacterial-genomes!67
epi2me-labs · May 17, 2023 · d3fdcc0 · d3fdcc0
2 parents bde5a30 + fd81890
commit d3fdcc0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [unreleased]
+## [v0.2.14]
 ### Added
 - `--isolates` parameter that will run the ResFinder tool on the final assembly to output antimicrobial resistance genes.
 - Configuration for running demo data in AWS

diff --git a/bin/workflow_glue/report.py b/bin/workflow_glue/report.py
@@ -63,7 +63,7 @@ def get_flye_stats(sample_names, flye_dir, flye_suffix):
     return flye_out
 
 
-def gather_sample_files(sample_names, denovo_mode, prokka_mode, resfinder_mode):
+def gather_sample_files(sample_names, denovo_mode, prokka_mode):
     """Collect files required for the report per sample and make sure they exist."""
     sample_files = {}
     subdirs_and_suffixes = {
@@ -86,13 +86,15 @@ def gather_sample_files(sample_names, denovo_mode, prokka_mode, resfinder_mode):
                 file_type in ("total_depth", "fwd_depth", "rev_depth")
                 or (file_type == "variants" and not denovo_mode)
                 or (file_type == "prokka" and prokka_mode)
-                or (file_type == "resfinder" and resfinder_mode)
             ):
                 if not os.path.exists(file):
                     raise ValueError(
                         f"Required file '{file_type}' missing "
                         f"for sample '{sample_name}'."
                     )
+            elif (file_type == "resfinder"):
+                if not os.path.exists(file):
+                    file = None
             else:
                 # this covers the cases when files are not needed (e.g. `variants` when
                 # doing a de-novo assembly)
@@ -282,7 +284,7 @@ def main(args):
     # Gather stats files for each sample (will be used by the various report sections
     # below)
     sample_files = gather_sample_files(
-        args.sample_ids, args.denovo, args.prokka, args.resfinder)
+        args.sample_ids, args.denovo, args.prokka)
 
     with report.add_section("Genome coverage", "Depth"):
         html_tags.p(
@@ -362,12 +364,16 @@ def main(args):
                             else None
                         )
                         # now the indel length histogram
-                        indel_lengths_df = bcf_stats["IDD"].query("sample == @sample")
-                        indel_hist = (
-                            get_indel_length_histogram(indel_lengths_df)
-                            if not indel_lengths_df.empty
-                            else None
-                        )
+                        indel_hist = None
+                        if (
+                            "IDD" in bcf_stats
+                            and not (
+                                indel_lengths_df := bcf_stats["IDD"].query(
+                                    "sample == @sample"
+                                )
+                            ).empty
+                        ):
+                            indel_hist = get_indel_length_histogram(indel_lengths_df)
                         with Grid():
                             if subst_heatmap is not None:
                                 EZChart(subst_heatmap, "epi2melabs")
@@ -416,11 +422,20 @@ def main(args):
             with tabs.add_dropdown_menu():
                 for name, files in sample_files.items():
                     with tabs.add_dropdown_tab(name):
-                        resfinder_df = pd.read_csv(
-                            files["resfinder"], sep='\t').rename(
-                            columns=lambda col: col[0].upper() + col[1:]
-                        )
-                        DataTable.from_pandas(resfinder_df, use_index=False)
+                        if files["resfinder"] is None:
+                            html_raw("""
+                <b>
+                Resfinder did not work for this sample.
+                Please check that species and reference parameters are relevant
+                to the sample.</b>
+                """)
+                        else:
+
+                            resfinder_df = pd.read_csv(
+                                files["resfinder"], sep='\t').rename(
+                                columns=lambda col: col[0].upper() + col[1:]
+                            )
+                            DataTable.from_pandas(resfinder_df, use_index=False)
     report.write(args.output)
     logger.info(f"Report written to {args.output}.")
 

diff --git a/main.nf b/main.nf
@@ -53,7 +53,6 @@ process deNovo {
         tuple val(meta), path("${meta.alias}.draft_assembly.fasta.gz"), path("${meta.alias}_flye_stats.tsv")
     script:
     """
-    echo memory: $task.memory
     flye --nano-raw reads.fastq.gz --out-dir output --threads "${task.cpus}"
     mv output/assembly.fasta "./${meta.alias}.draft_assembly.fasta"
     mv output/assembly_info.txt "./${meta.alias}_flye_stats.tsv"

diff --git a/modules/local/amr.nf b/modules/local/amr.nf
@@ -2,15 +2,15 @@
 
 process resfinderAcquiredOnly {
     label "amr"
-    containerOptions '--entrypoint=""'
+    errorStrategy 'ignore'
     input:
         tuple val(meta), path("input_genome.fasta.gz")
     output:
-        tuple val(meta), path("${meta.alias}_resfinder_results")
+        tuple val(meta), path("${meta.alias}_resfinder_results"), optional: true
     script:
     """
     gunzip -c input_genome.fasta.gz > input_genome.fasta
-    python -m resfinder --acquired -ifa input_genome.fasta --outputPath ${meta.alias}_resfinder_results 
+    python -m resfinder --acquired -ifa input_genome.fasta --outputPath ${meta.alias}_resfinder_results || exit 0
     """
 }
 
@@ -32,7 +32,7 @@ process processResfinderAquired {
 
 process resfinderFull {
     label "amr"
-    containerOptions '--entrypoint=""'
+    errorStrategy 'ignore'
     input:
         tuple val(meta), path("input_genome.fasta.gz")
         val species
@@ -54,7 +54,7 @@ process resfinderFull {
         -s "${species_input}" \
         --point \
         -ifa input_genome.fasta \
-        --disinfectant
+        --disinfectant || exit 0
     """
 }
 

diff --git a/nextflow.config b/nextflow.config
@@ -54,7 +54,7 @@ manifest {
     description     = 'Assembly, variant calling, and annotation of bacterial genomes.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = 'v0.2.13'
+    version         = 'v0.2.14'
 }
 
 epi2melabs {
@@ -83,6 +83,7 @@ process {
     }
     withLabel:amr {
         container = "genomicepidemiology/resfinder:${params.resfinder_version}"
+        containerOptions = {workflow.profile == "standard" ? "--entrypoint=''" : ""}
     }
     shell = ['/bin/bash', '-euo', 'pipefail']
 }