Long merge rsem

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [PR #1640](https://github.com/nf-core/rnaseq/pull/1640) - Bump version after release 3.22.0
 - [PR #1641](https://github.com/nf-core/rnaseq/pull/1641) - Add arm-based CI tests and fix arm-related issues
+- [PR #1642](https://github.com/nf-core/rnaseq/pull/1642) - Add long format to rsem merge
 
 ## [[3.22.0](https://github.com/nf-core/rnaseq/releases/tag/3.22.0)] - 2025-11-26
 
@@ -20,7 +21,7 @@ Special thanks to the following for their contributions to the release:
 
 - [Ahwan Pandey](https://github.com/ahwanpandey)
 - [Cristina Tuñí i Domínguez](https://github.com/ctuni)
-- [Elad Herzog](https://github.com/EladH1)
+- [Elad Herz](https://github.com/EladH1)
 - [Emily Miyoshi](https://github.com/emilymiyoshi)
 - [Jonathan Manning](https://github.com/pinin4fjords)
 - [Pontus Höjer](https://github.com/pontushojer)

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, and FPKM across all samples.
+  - `rsem.merged.isoforms_long.tsv`: long format contains length, expected_count, TPM, FPKM, and 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/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

@@ -1,4 +1,119 @@
 {
+    "homo_sapiens - sentieon - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "5": [
+                    "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "6": [
+                    "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "7": [
+                    "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "8": [
+                    "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
+                    "versions.yml:md5,773c15c4ecb7d486a4bdd8ef73e7ac5d"
+                ],
+                "counts_gene": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.genes.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "counts_transcript": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.isoforms.results:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "logs": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "merged_counts_gene": [
+                    "rsem.merged.gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "merged_counts_transcript": [
+                    "rsem.merged.transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "merged_tpm_gene": [
+                    "rsem.merged.gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "merged_tpm_transcript": [
+                    "rsem.merged.transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "stat": [
+                    [
+                        {
+                            "id": "test",
+                            "strandedness": "forward"
+                        },
+                        "test.stat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2aa5252eb2ffb409cf556a165d40f8a9",
+                    "versions.yml:md5,773c15c4ecb7d486a4bdd8ef73e7ac5d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-27T16:26:57.604104651"
+    },
     "homo_sapiens - stub": {
         "content": [
             {
@@ -109,10 +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": [
@@ -165,9 +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"
     }
 }