Long merge rsem

.github/workflows/linting.yml

@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: linting-logs
           path: |

docs/output.md

@@ -278,6 +278,8 @@ The STAR section of the MultiQC report shows a bar plot with alignment rates: go
   - `rsem.merged.gene_tpm.tsv`: Matrix of gene-level TPM values across all samples.
   - `rsem.merged.transcript_counts.tsv`: Matrix of isoform-level raw counts across all samples.
   - `rsem.merged.transcript_tpm.tsv`: Matrix of isoform-level TPM values across all samples.
+  - `rsem.merged.genes_long.tsv`: long format contains length, expected_count,TPM,FPKM across all samples.
+  - `rsem.merged.isoforms_long.tsv`: long format contains length, expected_count,TPM,FPKM,IsoPct across all samples.
   - `*.genes.results`: RSEM gene-level quantification results for each sample.
   - `*.isoforms.results`: RSEM isoform-level quantification results for each sample.
   - `*.STAR.genome.bam`: If `--save_align_intermeds` is specified the BAM file from STAR alignment containing read alignments to the reference genome will be placed in this directory. These files can be reused as `genome_bam` input in future pipeline runs.

modules/local/rsem_merge_counts/main.nf

@@ -15,6 +15,8 @@ process RSEM_MERGE_COUNTS {
     path "rsem.merged.gene_tpm.tsv"         , emit: tpm_gene
     path "rsem.merged.transcript_counts.tsv", emit: counts_transcript
     path "rsem.merged.transcript_tpm.tsv"   , emit: tpm_transcript
+    path "rsem.merged.genes_long.tsv"       , emit: genes_long
+    path "rsem.merged.isoforms_long.tsv"    , emit: isoforms_long
     path "versions.yml"                     , emit: versions
 
     when:
@@ -47,6 +49,20 @@ process RSEM_MERGE_COUNTS {
     paste transcript_ids.txt tmp/isoforms/*.counts.txt > rsem.merged.transcript_counts.tsv
     paste transcript_ids.txt tmp/isoforms/*.tpm.txt > rsem.merged.transcript_tpm.tsv
 
+    # Create long format for genes (idx=1-4, concat columns 5-7)
+    echo -e "sample_name\tgene_id\ttranscript_id(s)\tlength\teffective_length\texpected_count\tTPM\tFPKM" > rsem.merged.genes_long.tsv
+    for fileid in `ls ./genes/*`; do
+        samplename=`basename \$fileid | sed s/\\.genes.results\$//g`
+        tail -n+2 \$fileid | awk -v sample=\$samplename 'BEGIN{OFS="\t"}{print sample,\$1,\$2,\$3,\$4,\$5,\$6,\$7}' >> rsem.merged.genes_long.tsv
+    done
+
+    # Create long format for isoforms (idx=1-4, concat columns 5-8)
+    echo -e "sample_name\ttranscript_id\tgene_id\tlength\teffective_length\texpected_count\tTPM\tFPKM\tIsoPct" > rsem.merged.isoforms_long.tsv
+    for fileid in `ls ./isoforms/*`; do
+        samplename=`basename \$fileid | sed s/\\.isoforms.results\$//g`
+        tail -n+2 \$fileid | awk -v sample=\$samplename 'BEGIN{OFS="\t"}{print sample,\$1,\$2,\$3,\$4,\$5,\$6,\$7,\$8}' >> rsem.merged.isoforms_long.tsv
+    done
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
@@ -59,6 +75,8 @@ process RSEM_MERGE_COUNTS {
     touch rsem.merged.gene_tpm.tsv
     touch rsem.merged.transcript_counts.tsv
     touch rsem.merged.transcript_tpm.tsv
+    touch rsem.merged.genes_long.tsv
+    touch rsem.merged.isoforms_long.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/rsem_merge_counts/test_local.nf

@@ -0,0 +1,16 @@
+#! /usr/bin/env nextflow
+
+// /home/eladh/code/development/NF-core/nf-core-rnaseq_3.21.0/3_21_0/modules/local/rsem_merge_counts/genes
+// /home/eladh/code/development/NF-core/nf-core-rnaseq_3.21.0/3_21_0/modules/local/rsem_merge_counts/isoforms
+
+nextflow.enable.dsl=2
+include {RSEM_MERGE_COUNTS} from './main.nf'
+
+
+
+workflow  {
+
+    RSEM_MERGE_COUNTS(Channel.fromPath(params.genes), Channel.fromPath(params.isoforms))
+
+
+}

modules/local/rsem_merge_counts/tests/main.nf.test.snap

@@ -15,6 +15,12 @@
                     "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "4": [
+                    "rsem.merged.genes_long.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "5": [
+                    "rsem.merged.isoforms_long.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "6": [
                     "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
                 ],
                 "counts_gene": [
@@ -23,6 +29,12 @@
                 "counts_transcript": [
                     "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
+                "genes_long": [
+                    "rsem.merged.genes_long.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "isoforms_long": [
+                    "rsem.merged.isoforms_long.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
                 "tpm_gene": [
                     "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
@@ -35,10 +47,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-06-21T11:55:29.45389"
+        "timestamp": "2025-11-27T17:09:36.795867708"
     },
     "Should run without failures": {
         "content": [
@@ -56,6 +68,12 @@
                     "rsem.merged.transcript_tpm.tsv:md5,abbaac45f9938716c58d604299ea284e"
                 ],
                 "4": [
+                    "rsem.merged.genes_long.tsv:md5,e26cd2b3b381432a011eed98f3ad4e6d"
+                ],
+                "5": [
+                    "rsem.merged.isoforms_long.tsv:md5,33b189595600493b917d786a542de8e9"
+                ],
+                "6": [
                     "versions.yml:md5,48ca3e12c91829af8019462b3f6aa29c"
                 ],
                 "counts_gene": [
@@ -64,6 +82,12 @@
                 "counts_transcript": [
                     "rsem.merged.transcript_counts.tsv:md5,e40bba0aafc5904361513b3513c217ad"
                 ],
+                "genes_long": [
+                    "rsem.merged.genes_long.tsv:md5,e26cd2b3b381432a011eed98f3ad4e6d"
+                ],
+                "isoforms_long": [
+                    "rsem.merged.isoforms_long.tsv:md5,33b189595600493b917d786a542de8e9"
+                ],
                 "tpm_gene": [
                     "rsem.merged.gene_tpm.tsv:md5,39bad606eb012456bba1d995fe0feb5f"
                 ],
@@ -76,9 +100,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-03-09T17:13:37.377348"
+        "timestamp": "2025-11-27T17:09:28.461621756"
     }
 }

subworkflows/local/quantify_rsem/tests/main.nf.test.snap

@@ -109,10 +109,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-15T16:59:19.581004"
+        "timestamp": "2025-11-27T16:26:57.604104651"
     },
     "homo_sapiens - stub": {
         "content": [
@@ -224,10 +224,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
+            "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-15T16:56:01.229068"
+        "timestamp": "2025-11-27T16:26:03.792661891"
     },
     "homo_sapiens": {
         "content": [
@@ -280,9 +280,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-16T08:19:00.078928064"
+        "timestamp": "2025-11-27T17:10:37.825495549"
     }
 }