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Restore modkit test with smaller gtf, fix join error

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This commit is contained in:
Sam Nicholls 2026-05-26 20:12:45 +00:00
parent e95b51016a
commit b6f9efd9ae
3 changed files with 19 additions and 11 deletions
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11
.gitlab-ci.yml
View File

@ -69,7 +69,7 @@ docker-run:
- MATRIX_NAME: [
"int_discover_dna", "int_fixed_rna", "int_de_control_vs_control",
"smoke_discover", "smoke_fixed", "smoke_direct_rna", "smoke_de",
"mouse_de_0countquant"
"mouse_de_0countquant", "mods_bigwig_igv"
]
rules:
# NOTE As we're overriding the rules block for the included docker-run
@ -181,6 +181,15 @@ docker-run:
--de_analysis --ref_genome ${CI_PROJECT_NAME}/data/mouse_subset_test/mouse_subset.fa \
--ref_annotation ${CI_PROJECT_NAME}/data/mouse_subset_test/mouse_subset.gtf.gz \
--direct_rna --sample_sheet ${CI_PROJECT_NAME}/data/mouse_subset_test/sample_sheet.csv"
# MM/ML tag test
- if: $MATRIX_NAME == "mods_bigwig_igv"
variables:
NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -nv https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/mods_rna_subset.tar.gz -O ${CI_PROJECT_NAME}/data/mods_rna_subset.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/mods_rna_subset.tar.gz -C ${CI_PROJECT_NAME}/data/ && wget -nv https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf -O ${CI_PROJECT_NAME}/data/gencode.v22.annotation.chr20.gtf && wget -nv https://ont-open-data.s3.amazonaws.com/references/human/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz -O ${CI_PROJECT_NAME}/data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz"
NF_WORKFLOW_OPTS: "--bam ${CI_PROJECT_NAME}/data/mods_rna_subset/ \
--ref_genome ${CI_PROJECT_NAME}/data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
--ref_annotation ${CI_PROJECT_NAME}/data/gencode.v22.annotation.chr20.gtf \
--sample_sheet ${CI_PROJECT_NAME}/data/mods_rna_subset/sample_sheet.csv \
--igv"
singularity-run:

2
main.nf
View File

@ -204,7 +204,7 @@ workflow {
"output_cache": false,
"output_mmi": false,
])
ref_genome = prepared_reference.ref_tuple
ref_genome = prepared_reference.ref_tuple.first()
if (!ref_annotation.exists()) {
throw new Exception("--ref_annotation does not exist.")

17
subworkflows/transcriptome.nf
View File

@ -222,7 +222,6 @@ workflow transcriptome_analysis {
}
}
analysis_annotation = prepared_reference_annotation.annotation.first()
analysis_reference = ref_genome.first()
joint_meta = [alias: "cohort"]
joint_discover = runJointBambuDiscover(
@ -241,14 +240,14 @@ workflow transcriptome_analysis {
)
},
analysis_annotation,
analysis_reference
ref_genome
)
joint_quant_inputs_all = bambu_discover_to_quant_inputs(joint_discover.dir)
joint_quant = runJointBambuQuant(
bambu_quant_process_inputs(
bambu_filter_quant_inputs_with_warning(joint_quant_inputs_all)
),
analysis_reference
ref_genome
)
joint_bambu_real = collateJointBambuQuant(
joint_quant.dir
@ -284,14 +283,14 @@ workflow transcriptome_analysis {
)
},
analysis_annotation,
analysis_reference
ref_genome
)
sample_quant_inputs_all = bambu_discover_to_quant_inputs(sample_discover.dir)
sample_quant = runPerSampleBambuQuant(
bambu_quant_process_inputs(
bambu_filter_quant_inputs_with_warning(sample_quant_inputs_all)
),
analysis_reference
ref_genome
)
sample_bambu_real = collatePerSampleBambuQuant(
sample_quant.dir
@ -318,9 +317,9 @@ workflow transcriptome_analysis {
joint_fasta = buildCohortTranscriptomeFasta(
joint_bambu_real.gtf.map { meta, gtf -> gtf },
analysis_reference
ref_genome
)
sample_fastas = buildSampleTranscriptomeFasta(sample_bambu_real.gtf, analysis_reference)
sample_fastas = buildSampleTranscriptomeFasta(sample_bambu_real.gtf, ref_genome)
if (params.skip_sqanti) {
joint_sqanti_dir = Channel.empty()
@ -329,9 +328,9 @@ workflow transcriptome_analysis {
joint_sqanti = runJointSqanti(
joint_bambu_real.gtf.map { meta, gtf -> gtf },
analysis_annotation,
analysis_reference
ref_genome
)
sample_sqanti = runPerSampleSqanti(sample_bambu_real.gtf, analysis_annotation, analysis_reference)
sample_sqanti = runPerSampleSqanti(sample_bambu_real.gtf, analysis_annotation, ref_genome)
joint_sqanti_dir = joint_sqanti.dir
sample_sqanti_dirs = sample_sqanti.dir
}