Cache resume broken when changing syntax parser. #6788
Description
Bug report
Running the same pipeline with resume with different syntax parser generates different hash.
Expected behavior and actual behavior
Task hash should be the same in both parsers
Steps to reproduce the problem
Run the rnaseq-nf pipeline with 25.10.3 and master (V2 default) and with NXF_SYNTAX_PARSER=v1
Program output
Stable version:
$ NXF_VER=25.10.3 nextflow run rnaseq-nf -profile docker -resume
N E X T F L O W ~ version 25.10.3
Launching `https://github.com/nextflow-io/rnaseq-nf` [small_jang] DSL2 - revision: ca20a6dfd2 [master]
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: /home/jorgee/.nextflow/assets/nextflow-io/rnaseq-nf/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
reads : /home/jorgee/.nextflow/assets/nextflow-io/rnaseq-nf/data/ggal/ggal_gut_{1,2}.fq
outdir : results
[46/65f5d4] process > RNASEQ:INDEX (ggal_1_48850000_49020000) [100%] 1 of 1, cached: 1 ✔
[ba/dfa2cb] process > RNASEQ:FASTQC (ggal_gut) [100%] 1 of 1, cached: 1 ✔
[33/442d00] process > RNASEQ:QUANT (ggal_gut) [100%] 1 of 1, cached: 1 ✔
[ee/c19570] process > MULTIQC [100%] 1 of 1, cached: 1 ✔
Done! Open the following report in your browser --> results/multiqc_report.html
In master branch with V1 parser, the cache works.
$ NXF_SYNTAX_PARSER=v1 dev_nextflow run rnaseq-nf -profile docker -resume
N E X T F L O W ~ version 25.12.0-edge
Launching `https://github.com/nextflow-io/rnaseq-nf` [magical_wiles]revision: ca20a6dfd2 [master]
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: /home/jorgee/.nextflow/assets/.repos/nextflow-io/rnaseq-nf/clones/ca20a6dfd2d799b903e557dc2e736d55419c7a1a/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
reads : /home/jorgee/.nextflow/assets/.repos/nextflow-io/rnaseq-nf/clones/ca20a6dfd2d799b903e557dc2e736d55419c7a1a/data/ggal/ggal_gut_{1,2}.fq
outdir : results
[46/65f5d4] process > RNASEQ:INDEX (ggal_1_48850000_49020000) [100%] 1 of 1, cached: 1 ✔
[ba/dfa2cb] process > RNASEQ:FASTQC (ggal_gut) [100%] 1 of 1, cached: 1 ✔
[33/442d00] process > RNASEQ:QUANT (ggal_gut) [100%] 1 of 1, cached: 1 ✔
[ee/c19570] process > MULTIQC [100%] 1 of 1, cached: 1 ✔
Done! Open the following report in your browser --> results/multiqc_report.html
In master branch with V2 parser (default), it doesn't detect the cached tasks.
$ dev_nextflow run rnaseq-nf -profile docker -resume
N E X T F L O W ~ version 25.12.0-edge
Launching `https://github.com/nextflow-io/rnaseq-nf` [hungry_jepsen]revision: ca20a6dfd2 [master]
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: /home/jorgee/.nextflow/assets/.repos/nextflow-io/rnaseq-nf/clones/ca20a6dfd2d799b903e557dc2e736d55419c7a1a/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
reads : /home/jorgee/.nextflow/assets/.repos/nextflow-io/rnaseq-nf/clones/ca20a6dfd2d799b903e557dc2e736d55419c7a1a/data/ggal/ggal_gut_{1,2}.fq
outdir : results
executor > local (4)
[b3/cf307d] process > RNASEQ:INDEX (ggal_1_48850000_49020000) [100%] 1 of 1 ✔
[eb/ffe39b] process > RNASEQ:FASTQC (ggal_gut) [100%] 1 of 1 ✔
[4f/db0476] process > RNASEQ:QUANT (ggal_gut) [100%] 1 of 1 ✔
[b9/20d9d0] process > MULTIQC [100%] 1 of 1 ✔
Done! Open the following report in your browser --> results/multiqc_report.html
Inspecting with lineage diff it is caused by the task code hash
@@ -5,7 +5,7 @@
"sessionId": "4ad8ce27-4f7e-41a2-89ff-1b2c4bf822f0",
"name": "RNASEQ:INDEX (ggal_1_48850000_49020000)",
"codeChecksum": {
- "value": "46f671c122f3efdbc6ce16e44cca417e",
+ "value": "39922d6ff918b5b841ab062e56dcff5f",
"algorithm": "nextflow",
"mode": "standard"
},
Environment
- Nextflow version: 25.10.x and master
- Java version: 21
- Operating system: Linux