HannahBenisty commented 1 year ago

Ask away!

Hi! Usually a read summary appears in the read report, but now I have a run with 24 barcodes and the report starts at the lineages. It would be great if we could also see the read summary. Is there a way to find this information in other documents generated with this workflow. Many thanks!

nggvs commented 1 year ago

Hi! Thanks for using the workflow. Which version of the wf-metagenomics are you using and which options?

HannahBenisty commented 1 year ago

Hi, I am using minimap2 as classifier and added the option minimap2_by_reference. The version is the last one which I dowloaded using git clone gh repo clone epi2me-labs/wf-metagenomics.

nggvs commented 1 year ago

Ok, thank you very much! I will try to reproduce it (v2.0.7). Could you run the workflow using demo or test_data to see if you also observe the same issue?

HannahBenisty commented 1 year ago

I have run a test data case 01 with the following options: --fastq test_data/case01/ --classifier minimap2 --minimap2_by_reference. Read summary not appearing.

nggvs commented 1 year ago

I'm trying to reproduce the error, but I see this using test_data or demo data with the latest version.

So, I'm not sure of what could be happening. Are you getting any error when you run the workflow? Could you paste the log?

HannahBenisty commented 1 year ago

Hi,

here are the options I have used and the log: --fastq test_data/case01/ --classifier minimap2 --minimap2_by_reference

N E X T F L O W ~ version 23.04.3 Launching main.nf [trusting_panini] DSL2 - revision: f09278680a WARN: NEXTFLOW RECURSION IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES

WARN: Found unexpected parameters:

--watch_path: false
--bracken_dist: null [2m- Ignore this warning: params.schema_ignore_params = "watch_path,bracken_dist" [0m

[0;92m|||||||||| [0m[2m_ __ _ __ ____ [0;92m|||||||||| [0m[2m| ____| _ | | \/ | __| | | | | [0;33m||||| [0m[2m| | | |) | | ) | |\/| | _| ___| |/ ` | ' \/ | [0;33m||||| [0m[2m| |_| /| | / /| | | | |_|| | (| | |) _ \ [0;94m|||||||||| [0m[2m|____|_| |_|___|| ||| ||\,|._/|/ [0;94m|||||||||| [0m[1mwf-metagenomics v2.6.1[0m [2m--------------------------------------------------------------------------------[0m [1mCore Nextflow options[0m [0;34mrunName : [0;32mtrusting_panini[0m [0;34mcontainerEngine : [0;32msingularity[0m [0;34mlaunchDir : [0;32m/nfs/users/rg/hbenisty/wf-meta/test_nat/wf-metagenomics[0m [0;34mworkDir : [0;32m/nfs/users/rg/hbenisty/wf-meta/test_nat/wf-metagenomics/work[0m [0;34mprojectDir : [0;32m/nfs/users/rg/hbenisty/wf-meta/test_nat/wf-metagenomics[0m [0;34muserName : [0;32mhbenisty[0m [0;34mprofile : [0;32mcrg[0m [0;34mconfigFiles : [0;32m/nfs/users/rg/hbenisty/wf-meta/test_nat/wf-metagenomics/nextflow.config[0m

[1mInput Options[0m [0;34mfastq : [0;32mtest_data/case01/[0m [0;34mclassifier : [0;32mminimap2[0m

[1mMinimap2 Options[0m [0;34msplit_prefix : [0;32mtrue[0m [0;34mminimap2_by_reference: [0;32mtrue[0m

!! Only displaying parameters that differ from the pipeline defaults !! [2m--------------------------------------------------------------------------------[0m If you use epi2me-labs/wf-metagenomics for your analysis please cite:

The nf-core framework https://doi.org/10.1038/s41587-020-0439-x

[2m--------------------------------------------------------------------------------[0m This is epi2me-labs/wf-metagenomics v2.6.1. [2m--------------------------------------------------------------------------------[0m Checking inputs. WARN: Access to undefined parameter real_time -- Initialise it to a default value eg. params.real_time = some_value Minimap2 pipeline. Preparing databases. Using default taxonomy database. Using a default database. Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files. [skipping] Stored process > prepare_databases:download_reference_ref2taxid [skipping] Stored process > prepare_databases:download_unpack_taxonomy [6c/ecf4cd] Cached process > fastcat (3) [6b/6e745d] Cached process > fastcat (2) [91/a2d0d9] Cached process > fastcat (1) [d4/ce9fbc] Cached process > minimap_pipeline:run_common:getVersions [30/6c5f96] Cached process > minimap_pipeline:run_common:getParams [c9/fce416] Cached process > minimap_pipeline:output (1) [f5/bfa54f] Submitted process > minimap_pipeline:output (2) [ff/a6b2d1] Submitted process > minimap_pipeline:minimap (1) [b7/311ecf] Submitted process > minimap_pipeline:minimap (3) [4b/6f488f] Submitted process > minimap_pipeline:minimap (2) [f8/7b4c42] Submitted process > minimap_pipeline:getAlignmentStats (1) [26/228e71] Submitted process > minimap_pipeline:getAlignmentStats (2) [b0/ce42f0] Submitted process > minimap_pipeline:getAlignmentStats (3) [5a/e02886] Submitted process > minimap_pipeline:createAbundanceTables [41/d851ce] Submitted process > minimap_pipeline:output (3) [a1/a95d25] Submitted process > minimap_pipeline:makeReport (1) [34/1d4090] Submitted process > minimap_pipeline:output (4)

nggvs commented 1 year ago

Hi, Thank you for the log. From it I think you are using an old version of the workflow. Could you make sure you are using v2.7.0 and the master branch?

HannahBenisty commented 1 year ago

Ah ok, so I was using doing git clone from the link of the main page of the workflow.

git clone https://github.com/epi2me-labs/wf-metagenomics.git

Which link should I use? Thanks!

nggvs commented 1 year ago

That is correct, would you mind to go into the folder wf-metagenomics that has been downloaded and run this? git status

HannahBenisty commented 1 year ago

On branch master

Changes not staged for commit:

(use "git add ..." to update what will be committed)

(use "git checkout -- ..." to discard changes in working directory)

#

modified: nextflow.config

modified: subworkflows/minimap_pipeline.nf

#

Untracked files:

(use "git add ..." to include in what will be committed)

#

._log

._nextflow.config

log

output/

store_dir/

subworkflows/._minimap_pipeline.nf

work/

no changes added to commit (use "git add" and/or "git commit -a")

HannahBenisty commented 1 year ago

Hi Natalia,

I have tried again, and it works. Probably it was my fault because of messing with versions the nextflow config file.

nggvs commented 1 year ago

Hi @HannahBenisty ,

Glad to hear that! I would suggest to:

git checkout -- nextflow.config
git checkout -- subworkflows/minimap_pipeline.nf

and then remove temporal files (subworkflows/._minimap_pipeline.nf, ._log, ._nextflow.config) to avoid any other issue. Then you can run git pull to make sure everything is fine and you have the latest stable version.

Besides, if you don't mind to close the issue (if it has been already solved), I would appreciate it!

epi2me-labs / wf-metagenomics

html report - read summary #74

Ask away!

On branch master

Changes not staged for commit:

(use "git add ..." to update what will be committed)

(use "git checkout -- ..." to discard changes in working directory)

modified: nextflow.config

modified: subworkflows/minimap_pipeline.nf

Untracked files:

(use "git add ..." to include in what will be committed)

._log

._nextflow.config

log

output/

store_dir/

subworkflows/._minimap_pipeline.nf

work/