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nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
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Force dsl1 from config #46

Closed dhoogest closed 2 years ago

dhoogest commented 2 years ago

With versions of nextflow >= 22.03, DSL2 is the default syntax (see here). This creates problems for the current main.nf, specifically .into():

nextflow run https://github.com/nhoffman/dada2-nf -revision master -latest -profile singularity -params-file configs/params.json
NOTE: Nextflow is not tested with Java 1.8.0_312 -- It's recommended the use of version 11 up to 18

N E X T F L O W ~ version 22.04.0
Pulling nhoffman/dada2-nf ...
Already-up-to-date
WARN: It appears you have never run this project before -- Option `-resume` is ignored
Launching `[https://github.com/nhoffman/dada2-nf`](https://github.com/nhoffman/dada2-nf%60) [adoring_banach] DSL2 - revision: ee1c4bf2e1 [master]
Operator `into` has been deprecated -- it's not available in DSL2 syntax

-- Check script '/mnt/home/dhoogest/.nextflow/assets/nhoffman/dada2-nf/main.nf' at line: 27 or see '.nextflow.log' file for more details

Modification of the top level nextflow config here forces use of DSL=1, which I think will be needed until such time as we update the main.nf script.

Downloading nextflow-latest in a temp dir then running tests should reproduce the error, and confirm the fix here once branch is checked out.

/cc @mwohl

dhoogest commented 2 years ago

To reproduce (note comments related to DSL):

dhoogest@gattaca:~$ git clone git@github.com:nhoffman/dada2-nf.git dada2-nf-tmp
dhoogest@gattaca:~$ cd dada2-nf-tmp/
dhoogest@gattaca:~/dada2-nf-tmp$ wget -qO- https://get.nextflow.io | bash
dhoogest@gattaca:~/dada2-nf-tmp$ ./nextflow run main.nf -params-file params-minimal.json -profile singularity
NOTE: Nextflow is not tested with Java 1.8.0_312 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.0
WARN: It appears you have never run this project before -- Option `-resume` is ignored
Launching `main.nf` [jolly_dalembert] DSL2 - revision: ed64180d6c
Operator `into` has been deprecated -- it's not available in DSL2 syntax

 -- Check script 'main.nf' at line: 27 or see '.nextflow.log' file for more details
dhoogest@gattaca:~/dada2-nf-tmp$ git checkout force-dsl-1
Branch 'force-dsl-1' set up to track remote branch 'force-dsl-1' from 'origin'.
Switched to a new branch 'force-dsl-1'
dhoogest@gattaca:~/dada2-nf-tmp$ ./nextflow run main.nf -params-file params-minimal.json -profile singularity
NOTE: Nextflow is not tested with Java 1.8.0_312 -- It's recommended the use of version 11 up to 18

N E X T F L O W  ~  version 22.04.0
Launching `main.nf` [high_mccarthy] DSL1 - revision: ed64180d6c
[-        ] process > copy_filelist      -
[-        ] process > read_manifest      -
[-        ] process > copy_filelist      -
[-        ] process > read_manifest      -
[-        ] process > plot_quality       -
[-        ] process > barcodecop_dual    -
[-        ] process > bcop_counts_concat -
[-        ] process > filter_and_trim    -
[-        ] process > learn_errors       -
[-        ] process > dada_dereplicate   -
[-        ] process > combined_overlaps  -
[-        ] process > dada_counts_concat -
[-        ] process > write_seqs         -
[-        ] process > cmsearch           -
[-        ] process > filter_svs         -
[-        ] process > join_counts        -
[-        ] process > save_params        -
Pulling Singularity image library://nhoffman/dada2-nf/dada2-nf:v1.15 [cache /mnt/home/dhoogest/dada2-nf-tmp/work/singularity/nhoffman-dada2-nf-dada2-nf-v1.15.img]
nhoffman commented 2 years ago

Thanks @dhoogest - merging