Merge branch 'fix-ci-test-2' into 'dev'

Restore modkit test with smaller gtf, fix join error

See merge request epi2melabs/workflows/wf-transcriptomes!305

.gitlab-ci.yml

@@ -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:

main.nf

@@ -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.")

subworkflows/transcriptome.nf

@@ -222,7 +222,6 @@ workflow transcriptome {
             }
         }
         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_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_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 {
 
         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 {
             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
         }