Dev

CHANGELOG.md

@@ -3,6 +3,29 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.3.0] - 2024-07-04
+
+### `Changed`
+
+- Reformatted QCSummary fields and added a QCMessage field containing the old summary message. See [PR 85](https://github.com/phac-nml/mikrokondo/pull/85)
+
+- Changed default Python3 image to use the StarAMR image. See [PR 90](https://github.com/phac-nml/mikrokondo/pull/90)
+
+- Stripped identifier from taxonomic identification from string. See [PR 90](https://github.com/phac-nml/mikrokondo/pull/90)
+
+- Removed retry logic from processes and switched them to ignore. See [PR 91](https://github.com/phac-nml/mikrokondo/pull/91)
+
+### `Fixed`
+
+- Updated samtools/minimap2 container fixing CI issues and issues running the pipeline with Docker. See [PR 85](https://github.com/phac-nml/mikrokondo/pull/85)
+
+- Removed task.maxRetries from error handling to prevent StackOverflow addressing [PR 91](https://github.com/phac-nml/mikrokondo/pull/91)
+
+### `Added`
+
+- Altered name of stored `SpeciesTopHit` field in the irida-next.config, and added a field displaying the field name used addressing [PR 90](https://github.com/phac-nml/mikrokondo/pull/90)
+
+
 ## [0.2.1] - 2024-06-03
 
 ### `Fixed`
@@ -87,6 +110,7 @@ Initial release of phac-nml/mikrokondo. Mikrokondo currently supports: read trim
 
 - Added integration testing using [nf-test](https://www.nf-test.com/).
 
+[0.3.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.3.0
 [0.2.1]: https://github.com/phac-nml/mikrokondo/releases/tag/0.2.1
 [0.2.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.2.0
 [0.1.2]: https://github.com/phac-nml/mikrokondo/releases/tag/0.1.2

bin/report_summaries.py

@@ -6,7 +6,7 @@
 Matthew Wells: 2023-09-22
 """
 from dataclasses import dataclass
-from typing import Dict, Union
+from typing import Dict, Optional
 from collections import defaultdict
 import os
 import argparse
@@ -22,14 +22,16 @@ class CleaningInfo:
     trim_field int: when split on a delimiter which section of the list to keep
     """
     field: str
-    keep: Union[str, None] = None
-    trim_field: Union[int, None] = None
+    keep: Optional[str] = None
+    trim_field: Optional[int] = None
 
 class JsonImport:
     """Intake json report to convert to CSV"""
 
     __key_order = {v.field: v for v in [CleaningInfo(field="QCStatus"),
                 CleaningInfo(field="QCSummary"),
+                CleaningInfo(field="QCParameterSelection"),
+                CleaningInfo(field="QCMessage"),
                 CleaningInfo(field="QualityAnalysis", keep="message", trim_field=1),
                 CleaningInfo(field="meta")]}
     __keep_keys = frozenset(__key_order.keys())

conf/irida_next.config

@@ -62,7 +62,8 @@ iridanext {
                     "QualityAnalysis.nr_contigs.value"               : "nr contigs Value",
                     "QCSummary"                                      : "QC Summary",
                     "meta.downsampled"                               : "Downsampled",
-                    "SpeciesTopHit"                                  : "Species",
+                    "SpeciesTopHit"                                  : "predicted_identification_name",
+                    "IdentificationMethod"                           : "predicted_identification_method",
                     "ECTyperSubtyping.0.Database"                    : "ECTyper Database",
                     "ECTyperSubtyping.0.Evidence"                    : "ECTyper Evidence",
                     "ECTyperSubtyping.0.GeneCoverages(%)"            : "ECTyper GeneCoverages (%)",
@@ -128,6 +129,7 @@ iridanext {
                 ]
                 keep = [
                     "QCStatus",
+                    "QCSummary",
                     "QualityAnalysis.checkm_contamination.qc_status",
                     "QualityAnalysis.checkm_contamination.value",
                     "QualityAnalysis.average_coverage.qc_status",
@@ -140,7 +142,7 @@ iridanext {
                     "QualityAnalysis.length.value",
                     "QualityAnalysis.nr_contigs.qc_status",
                     "QualityAnalysis.nr_contigs.value",
-                    "QCSummary",
+                    "IdentificationMethod",
                     "meta.downsampled",
                     "SpeciesTopHit",
                     "ECTyperSubtyping.0.Database",

conf/modules.config

@@ -337,7 +337,8 @@ process {
         ext.parameters = params.quast
         stageInMode = params.stage_in_mode
         // scratch = false
-        errorStrategy = { task.attempt <= task.maxRetries ? sleep(Math.pow(2, task.attempt) * 200 as long) &&  'retry' : 'ignore' }
+        //errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+        errorStrategy = 'ignore'
         maxForks = 10 // Quast can get overloaded by job subs, so needs to be limited
         publishDir = [
             [
@@ -356,7 +357,8 @@ process {
         //container = params.checkm.container
         ext.parameters = params.checkm
         stageInMode = params.stage_in_mode
-        errorStrategy = { task.attempt <= task.maxRetries ? sleep(Math.pow(2, task.attempt) * 200 as long) && 'retry' : 'finish' }
+        //errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+        errorStrategy = 'ignore'
         // scratch = false
         publishDir = [
             [
@@ -373,7 +375,8 @@ process {
         ext.args = ""
         //container = params.bandage.container
         ext.parameters = params.bandage
-        errorStrategy = { task.attempt <= task.maxRetries ? sleep(Math.pow(2, task.attempt) * 200 as long) && 'retry' : 'ignore' }
+        //errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+        errorStrategy = 'ignore'
         stageInMode = params.stage_in_mode
         // scratch = false
         publishDir = [
@@ -523,8 +526,8 @@ process {
 
     withName: MASH_SCREEN {
         def dir_out = null
-        errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long)
-            return 'retry' }
+        //errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+        errorStrategy = 'ignore'
         maxForks = 20
         maxErrors = 3
         ext.args = "-w"
@@ -567,7 +570,8 @@ process {
     }
 
     withName: FLYE_ASSEMBLE {
-        errorStrategy = { task.exitStatus in [140] ? 'retry' : 'ignore'}
+        //errorStrategy = { task.exitStatus in [140] ? 'retry' : 'ignore'}
+        errorStrategy = 'ignore'
         //container = params.flye.container
         ext.parameters = params.flye
         ext.args = params.flye.args
@@ -623,8 +627,8 @@ process {
         maxRetries = 3
         ext.args = ""
         ext.parameters = params.spades
+        //errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
         errorStrategy = 'ignore'
-        //errorStrategy = { task.attempt <= task.maxRetries && sleep(Math.pow(2, task.attempt) * 200 as long) ? 'retry' : 'ignore' }
         // scratch = false
         publishDir = [
             [
@@ -787,7 +791,8 @@ process {
         // scratch = false
         ext.parameters = params.pilon_iterative
         maxRetries = 3
-        errorStrategy = { task.attempt <= task.maxRetries ? sleep(Math.pow(2, task.attempt) * 200 as long) &&  'retry' : 'ignore' }
+        //errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+        errorStrategy = 'ignore'
         publishDir = [
             [
                 path: { ["${task.assembly_polishing_directory_name}", "Pilon", "Fasta"].join(File.separator) },

modules/local/report.nf

@@ -35,6 +35,7 @@ process REPORT{
     def data_stride = 3 // report values added in groups of three, e.g sample meta info, parameters, output file of interest
     def headers_list = 'headers' // ! TODO this string exists twice, need to fix that
     def arr_size = test_in.size()
+    def qc_species_tag = "QCParameterSelection"
     for(long i = 0; i < arr_size; i=i+data_stride){
         def meta_data = test_in[i]
         def report_tag = test_in[i+1]
@@ -76,8 +77,8 @@ process REPORT{
     def search_phrases = qc_params_species()
 
     // Add in quality information in place
-    generate_qc_data(sample_data, search_phrases)
-    create_action_call(sample_data)
+    generate_qc_data(sample_data, search_phrases, qc_species_tag)
+    create_action_call(sample_data, qc_species_tag)
 
 
     def json_converted_data = new JsonBuilder(sample_data).toPrettyString()
@@ -124,6 +125,7 @@ def generate_coverage_data(sample_data, bp_field, species){
             // Add fixed genome coverage for species if desired
             def species_data_pos = 1;
             if(base_counts_p
+                && species[species_data_pos] != null
                 && species[species_data_pos].containsKey("fixed_genome_size")
                 && species[species_data_pos].fixed_genome_size != null){
 
@@ -197,7 +199,7 @@ def populate_qual_message(qual_data){
 }
 
 // Action: Reisolate and resequence, resequence, all good.
-def create_action_call(sample_data){
+def create_action_call(sample_data, species_tag){
     /*Define criteria used to create base sketches
 
     TODO Need to test a falthrough sample (e.g. unspeciated to see what happens)
@@ -224,6 +226,9 @@ def create_action_call(sample_data){
 
 
     TODO creating a logic heavy function that needs to be refactored
+
+    For addressing the defect, the Passed and failed messeges have been broken up, all that remains is to have the
+    final summary, checks passed and checks failed
     */
 
     for(val in sample_data){
@@ -245,8 +250,7 @@ def create_action_call(sample_data){
                     final_message = "[FAILED] Sample was determined to be metagenomic, and this was not specied as" +
                     " a metagenomic run indicating contamination REISOLATION AND RESEQUENCING RECOMMENDED." +
                     "There is additionally a possibility that your sample could not be identified as it is novel and " +
-                    "not included in the mash sketch provided to the pipeline (however this would be very rare), "+
-                    "but if this is the case please disregard this message."
+                    "not included in the program used to taxonomically classify your pipeline (however this is an unlikely culprit)."
                 }
                 sample_data[val.key]["QCStatus"] = sample_status
                 sample_data[val.key]["QCSummary"] = final_message
@@ -279,7 +283,6 @@ def create_action_call(sample_data){
             if(!meta_data.assembly){
                 // We should have reads as we assembled it
                 if(qual_data && qual_data.containsKey("raw_average_quality") && !qual_data.raw_average_quality.status){
-                    //qual_message.add(params.QCReportFields.raw_average_quality.low_msg)
                     resequence += 1
                     checks_failed += 1
                 }else if (qual_data && (!qual_data.containsKey("raw_average_quality") || !qual_data.raw_average_quality.status)){
@@ -290,7 +293,7 @@ def create_action_call(sample_data){
                 checks += 1
 
                 if(qual_data && qual_data.containsKey("average_coverage") && !qual_data.average_coverage.status){
-                    //qual_message.add(params.QCReportFields.average_coverage.low_msg)
+
                     if(meta_data.downsampled){
                         qual_message.add("The sample may have been downsampled too aggressively, if this is the cause please re-run sample with a different target depth.")
                     }
@@ -341,7 +344,6 @@ def create_action_call(sample_data){
             checks += 1
 
 
-
             (reisolate, resequence) = n50_nrcontigs_decision(qual_data, nr_contigs_failed, n50_failed, qual_message, reisolate, resequence)
             //qual_message.add("Quality Conclusion")
 
@@ -364,17 +366,26 @@ def create_action_call(sample_data){
                 qual_message.add("[PASSED] All Checks passed")
                 sample_status = "PASSED"
             }
-            qual_message.add("Passed Tests: ${checks - checks_failed - checks_ignored}/${checks}")
 
+            def organism_criteria = sample_data[val.key][species_tag]
+            def tests_passed = "Passed Tests: ${checks - checks_failed - checks_ignored}/${checks}"
+            qual_message.add(tests_passed)
 
-            qual_message.add("Species ID: ${val.value[val.key][params.top_hit_species.report_tag]}")
+            def species_id = "Species ID: ${val.value[val.key][params.top_hit_species.report_tag]}"
+            qual_message.add(species_id)
 
             // Qual summary not final message
             final_message = qual_message.join("\n")
             def terminal_message = populate_qual_message(qual_data).join("\n")
             log.info "\n$val.key\n${terminal_message}\n${sample_status}\n${final_message}"
+
+            // Reseq recommended should go to a seperate field
+            // Requested output should be: [PASS|FAILED] Species ID: [species] [Tests passed] [Organism criteria available]
+            qc_message = "${sample_status} ${species_id}; ${tests_passed}; Organism QC Criteria: ${organism_criteria}"
+
+            sample_data[val.key]["QCSummary"] = qc_message
             sample_data[val.key]["QCStatus"] = sample_status
-            sample_data[val.key]["QCSummary"] = final_message
+            sample_data[val.key]["QCMessage"] = final_message
         }
 
 }
@@ -604,7 +615,8 @@ def get_species(value, search_phrases, shortest_token){
         shortest_token: contains values to scrub from value to be searched for
     */
 
-    def qc_data = null;
+
+    def qc_data = [params.QCReport.fallthrough.search, params.QCReport.fallthrough];
     if(value == null){
         return qc_data
     }
@@ -626,7 +638,6 @@ def get_species(value, search_phrases, shortest_token){
 def get_qc_data_species(value_data, qc_data){
     def quality_messages = [:]
 
-
     params.QCReportFields.each{
         k, v ->
         if(v.on){ // only use the fields specified in the config
@@ -649,7 +660,7 @@ def get_qc_data_species(value_data, qc_data){
     return quality_messages;
 }
 
-def generate_qc_data(data, search_phrases){
+def generate_qc_data(data, search_phrases, qc_species_tag){
     /*
     data: sample data in a LazyMap
     search_phrases: normalized search phrases from the nextflow.config
@@ -659,12 +670,13 @@ def generate_qc_data(data, search_phrases){
     def top_hit_tag = params.top_hit_species.report_tag;
     def quality_analysis = "QualityAnalysis"
     def shortest_token = get_shortest_token(search_phrases)
+    def species_tag_location = 0
     for(k in data){
         if(!k.value.meta.metagenomic){
             def species = get_species(k.value[k.key][top_hit_tag], search_phrases, shortest_token)
-            //generate_coverage_data(data[k.key], params.seqtk_size.report_tag, species) // update coverage first so its values can be used in generating qc messages
             generate_coverage_data(data[k.key], params.coverage_calc_fields.bp_field, species) // update coverage first so its values can be used in generating qc messages
             data[k.key][quality_analysis] = get_qc_data_species(k.value[k.key], species)
+            data[k.key][qc_species_tag] = species[species_tag_location]
         }else{
             data[k.key][quality_analysis] = ["Metagenomic": ["message": null, "status": false]]
             data[k.key][quality_analysis]["Metagenomic"].message = "The sample was determined to be metagenomic, summary metrics will not be generated" +
@@ -865,7 +877,7 @@ def table_values(file_path, header_p, seperator, headers=null){
         }
     }
 
-    return rows_list.indexed().collectEntries { idx, row -> 
+    return rows_list.indexed().collectEntries { idx, row ->
         [(idx): row.collectEntries { k, v -> [(k): replace_missing(v)] }]
     }
 }

nextflow.config

@@ -43,7 +43,7 @@ params {
     show_hidden_params = false
     validationS3PathCheck = true
     validationShowHiddenParams = false
-    validationSchemaIgnoreParams = 'abricate,locidex,assembly_status,bakta,bandage,checkm,chopper,contigs_too_short,coreutils,coverage_calc_fields,ectyper,fastp,fastqc,filtered_reads,flye,kat,kleborate,kraken,kraken_bin,kraken_species,lissero,mash,mash_meta,medaka,minimap2,mlst,mobsuite_recon,opt_platforms,pilon,pilon_iterative,pointfinder_db_tag,python3,QCReport,QCReport-fields,QCReportFields,quast,racon,raw_reads,report_aggregate,r_contaminants,samtools,seqkit,seqtk,seqtk_size,shigeifinder,sistr,spades,spatyper,staramr,subtyping_report,top_hit_species,unicycler'
+    validationSchemaIgnoreParams = 'top_hit_method,abricate,locidex,assembly_status,bakta,bandage,checkm,chopper,contigs_too_short,coreutils,coverage_calc_fields,ectyper,fastp,fastqc,filtered_reads,flye,kat,kleborate,kraken,kraken_bin,kraken_species,lissero,mash,mash_meta,medaka,minimap2,mlst,mobsuite_recon,opt_platforms,pilon,pilon_iterative,pointfinder_db_tag,python3,QCReport,QCReport-fields,QCReportFields,quast,racon,raw_reads,report_aggregate,r_contaminants,samtools,seqkit,seqtk,seqtk_size,shigeifinder,sistr,spades,spatyper,staramr,subtyping_report,top_hit_species,unicycler'
     validationFailUnrecognisedParams = false // for the qcreport fields
 
     // SKIP options
@@ -193,8 +193,8 @@ params {
 
     // Python container, May switch for pypy3
     python3 {
-        singularity = "docker.io/python:3.11.6"
-        docker = "docker.io/python:3.11.6"
+        singularity = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
+        docker = "quay.io/biocontainers/staramr:0.10.0--pyhdfd78af_0"
     }
 
     seqtk {
@@ -424,14 +424,14 @@ params {
         report_tag = "SpeciesTopHit"
     }
 
-    kraken_species {
-        report_tag = "Kraken2TopHit"
+    top_hit_method {
+        report_tag = "IdentificationMethod"
     }
 
     r_contaminants {
         // container contains minimap2 and samtools
-        singularity = "https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0"
-        docker = "quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:8f2087d838e5270cd83b5a016667234429f16eea-0"
+        singularity = "https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0"
+        docker = "quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:3161f532a5ea6f1dec9be5667c9efc2afdac6104-0"
         phix_fa = ""
         homo_sapiens_fa = ""
         pacbio_mg = ""
@@ -1083,7 +1083,7 @@ manifest {
     description     = """Mikrokondo"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.2.1'
+    version         = '0.3.0'
     defaultBranch   = 'main'
     doi             = ''
 }