Merge branch 'CW-2188-denovo-test' into 'dev'
CW-2188 add test for denovo plus warnings Closes CW-2188 See merge request epi2melabs/workflows/wf-transcriptomes!100
This commit is contained in:
Sarah Griffiths
commit
cb73e0a6cd
@ -45,7 +45,7 @@ docker-run:
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- MATRIX_NAME: [
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"fusions", "differential_expression", "isoforms",
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"only_differential_expression", "differential_expression_gff3",
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"ncbi_gzip"
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"ncbi_gzip", "denovo"
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]
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rules:
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# NOTE As we're overriding the rules block for the included docker-run
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@ -59,6 +59,10 @@ docker-run:
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NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \
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--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref
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- if: $MATRIX_NAME == "denovo"
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variables:
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NF_WORKFLOW_OPTS: "--fastq test_data/fastq/SIRV_E0_PCS109_50.fq.gz --transcriptome_source denovo"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,build_minimap_index
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- if: $MATRIX_NAME == "fusions"
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variables:
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NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz
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@ -4,7 +4,10 @@ All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [unreleased]
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## [v0.1.13]
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### Added
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- Handling for GFF3 reference_annotation file type.
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- Warning for the `--transcriptome_source` denovo pipeline option.
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### Changed
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- Enum choices are enumerated in the `--help` output
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- Enum choices are enumerated as part of the error message when a user has selected an invalid choice
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@ -12,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Fixed
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- Replaced `--threads` option in fastqingress with hardcoded values to remove warning about undefined `param.threads`
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- Fix for the `--transcriptome_source` denovo pipeline option.
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## [v0.1.12]
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### Added
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@ -7,7 +7,6 @@
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from collections import defaultdict
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import math
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from pathlib import Path
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import sys
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import matplotlib
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from matplotlib import pyplot as plt
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@ -18,10 +17,12 @@ from sklearn.metrics.cluster import (
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adjusted_rand_score, completeness_score,
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homogeneity_score, v_measure_score)
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from .util import wf_parser # noqa: ABS101
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from .util import wf_parser, get_named_logger # noqa: ABS101
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matplotlib.use('Agg')
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logger = get_named_logger("clustqual")
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def argparser():
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"""Argument parser for entrypoint."""
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@ -181,16 +182,15 @@ def compute_v_measure(clusters, classes):
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compl_score = completeness_score(class_list, cluster_list)
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homog_score = homogeneity_score(class_list, cluster_list)
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ari = adjusted_rand_score(class_list, cluster_list)
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sys.stdout("Not included in clustering but aligned:", len(not_clustered))
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sys.stdout(
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logger.info("Not included in clustering but aligned:", len(not_clustered))
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logger.info(
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"v:",
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v_score,
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"Completeness:",
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compl_score,
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"Homogeneity:",
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homog_score)
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sys.stdout(
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logger.info(
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"Nr reads clustered but unaligned "
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"(i.e., no class and excluded from v-measure): ",
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clustered_but_unaligned)
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@ -231,14 +231,14 @@ def compute_v_measure_non_singleton_classes(clusters, classes):
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homog_score = homogeneity_score(class_list, cluster_list)
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nr_filtered_classes = len(
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[1 for cl_id in classes_dict if len(classes_dict[cl_id]) >= 5])
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sys.stdout(
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logger.info(
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"NONTRIvIAL CLASSES: v:",
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v_score,
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"Completeness:",
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compl_score,
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"Homogeneity:",
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homog_score)
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sys.stdout("NUMBER OF CLASSES (FILTERED):", len(
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logger.info("NUMBER OF CLASSES (FILTERED):", len(
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[1 for cl_id in classes_dict if len(classes_dict[cl_id]) >= 5]))
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return v_score, compl_score, homog_score, nr_filtered_classes
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@ -268,20 +268,20 @@ def compute_v_measure_non_singletons(clusters, classes):
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class_list.append(classes[read])
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cluster_list.append(clusters[read])
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else:
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# sys.stdout("Read was clustered but unaligned:", read)
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logger.debug("Read was clustered but unaligned:", read)
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clustered_but_unaligned += 1
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v_score = v_measure_score(class_list, cluster_list)
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compl_score = completeness_score(class_list, cluster_list)
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homog_score = homogeneity_score(class_list, cluster_list)
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sys.stdout(
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logger.info(
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"NONTRIvIAL CLUSTERS: v:",
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v_score,
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"Completeness:",
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compl_score,
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"Homogeneity:",
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homog_score)
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sys.stdout(
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logger.info(
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"NONTRIvIAL CLUSTERS: Nr reads clustered but unaligned "
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"(i.e., no class and excluded from v-veasure): ",
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clustered_but_unaligned)
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@ -407,11 +407,11 @@ def get_cluster_information(clusters, classes):
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else:
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clustered_classes[class_id] += 1
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sys.stdout("UNCLUSTERED:", "Tot classes:", len(not_clustered_classes))
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sys.stdout("CLUSTERED:", "Tot classes:", len(clustered_classes))
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sys.stdout("MIXED:", "Tot classes containing both:", len(
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logger.info("UNCLUSTERED:", "Tot classes:", len(not_clustered_classes))
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logger.info("CLUSTERED:", "Tot classes:", len(clustered_classes))
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logger.info("MIXED:", "Tot classes containing both:", len(
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set(clustered_classes.keys()) & set(not_clustered_classes.keys())))
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sys.stdout("Total number of classes (unique gene ID):", total_nr_classes)
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logger.info("Total number of classes (unique gene ID):", total_nr_classes)
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return (
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total_nr_classes - len(singleton_classes),
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len(singleton_classes),
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@ -507,7 +507,7 @@ def main(args):
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non_singleton_clusters = total_nr_clusters - singleton_clusters
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sys.stdout(
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logger.info(
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"NONTRIVIAL CLUSTERS: ", (total_nr_clusters - singleton_clusters))
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outfile.write("CLUSTERS\n")
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7
main.nf
7
main.nf
@ -255,7 +255,7 @@ process run_gffcompare{
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script:
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def out_dir = "${sample_id}_gffcompare"
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if ( ref_annotation.name.startsWith('OPTIONAL_FILE') ){
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if (params.transcriptome_source == "denovo"){
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"""
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mkdir $out_dir
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"""
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@ -454,14 +454,14 @@ workflow pipeline {
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ref_transcriptome
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use_ref_ann
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main:
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if (params.ref_genome.toLowerCase().endsWith("gz")) {
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if (params.ref_genome && file(params.ref_genome).extension == "gz") {
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// gzipped ref not supported by some downstream tools
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// easier to just decompress and pass it around.
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ref_genome = decompress_ref(ref_genome)
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}else {
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ref_genome = Channel.fromPath(ref_genome)
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}
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if (params.ref_annotation.toLowerCase().endsWith("gz")) {
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if (params.ref_annotation && file(params.ref_annotation).extension == "gz") {
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// gzipped ref not supported by some downstream tools
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// easier to just decompress and pass it around.
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decompress_annot= decompress_annotation(ref_annotation)
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@ -519,6 +519,7 @@ workflow pipeline {
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if (params.transcriptome_source == "denovo"){
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log.info("Doing de novo assembly")
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log.info("WARNING: The `--transcriptome_source` denovo option may have unexpected results and errors. If possible it is preferable to use the reference-guided pipeline.")
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assembly = denovo_assembly(full_len_reads, ref_genome)
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} else {
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@ -116,7 +116,7 @@ manifest {
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description = 'Transcriptome analysis including gene fusions, differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
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mainScript = 'main.nf'
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nextflowVersion = '>=22.10.8'
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version = 'v0.1.12'
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version = 'v0.1.13'
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}
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executor {
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@ -178,12 +178,13 @@ process make_batches {
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then
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batch_size=$minimum_batch_size
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fi
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echo "Num bases: \$nr_bases";
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else
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batch_size=${params.isOnClust2_batch_size}
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fi
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echo "Batch size:\$batch_size";
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echo "Num bases: \$nr_bases";
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mkdir -p sorted; isONclust2 sort $params.isOnClust2_sort_options -v -o sorted $fastq;
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"""
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@ -199,7 +200,7 @@ process clustering() {
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tuple val(sample_id), path('isONcluster_ROOT.cer'), emit: root_cluster
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script:
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"""
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workflow-glue run_isonclust2 $sorted_batches
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workflow-glue run_isonclust2 --workdir .
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"""
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}
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@ -261,8 +262,7 @@ workflow denovo_assembly {
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cds_align(
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merge_cds.out.final_polished_cds
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.join(make_batches.out.sorted_reads_dir))
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if (!reference.name.startsWith('OPTIONAL_FILE')){
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if (params.ref_genome) {
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cluster_quality(reference, fastq_reads_fl
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.join(dump_clusters.out.final_clusters_dir))
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