Bulk change conda syntax for all modules #2654

drpatelh · 2022-12-13T19:10:36Z

See nf-core/tools#1952

maxulysse

LGTM, we should remove the enable conda params from the template before the next tools release though

maxulysse · 2022-12-13T19:20:09Z

modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf

@@ -2,9 +2,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY {
    tag "$meta.id"
    label 'process_single'

-    if(params.enable_conda){
-        error "Conda environments cannot be used for GATK4/DetermineGermlineContigPloidy at the moment. Please use docker or singularity containers."


Can we keep an error message when using conda?

Don't know. It has to be tested but this will only affect a small minority of modules so we can add that afterwards. All of the modules I removed it from can be found in the commits I labelled Remove error raise for modules that dont support conda above.

maxulysse · 2022-12-13T19:21:11Z

modules/nf-core/gatk4/cnnscorevariants/main.nf

@@ -3,9 +3,6 @@ process GATK4_CNNSCOREVARIANTS {
    label 'process_low'

    //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers."


Can we keep an error message when using conda?

maxulysse · 2022-12-13T19:21:53Z

modules/nf-core/flash/main.nf

@@ -2,6 +2,7 @@ process FLASH {
    tag "$meta.id"
    label 'process_medium'

+    conda "bioconda::flash=1.2.11"


There was no conda before?

maxulysse · 2022-12-13T19:22:16Z

modules/nf-core/fcs/fcsgx/main.nf

@@ -2,10 +2,6 @@ process FCS_FCSGX {
    tag "$meta.id"
    label 'process_low'

-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using the FCS tool. Please use docker or singularity containers."


Can we keep an error message when using conda?

maxulysse · 2022-12-13T19:22:25Z

modules/nf-core/fcs/fcsadaptor/main.nf

@@ -2,9 +2,6 @@ process FCS_FCSADAPTOR {
    tag "$meta.id"
    label 'process_low'

-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using the FCS tool. Please use docker or singularity containers."


Can we keep an error message when using conda?

maxulysse · 2022-12-13T19:23:47Z

modules/nf-core/deepvariant/main.nf

@@ -2,11 +2,6 @@ process DEEPVARIANT {
    tag "$meta.id"
    label 'process_medium'

-
-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used with DeepVariant at the moment. Please use Docker or Singularity containers."


Can we keep an error message when using conda?

maxulysse · 2022-12-13T19:24:44Z

modules/nf-core/cellranger/mkref/main.nf

@@ -2,9 +2,6 @@ process CELLRANGER_MKREF {
    tag "$fasta"
    label 'process_high'

-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."


Can we keep an error message when using conda?

maxulysse · 2022-12-13T19:24:52Z

modules/nf-core/cellranger/mkgtf/main.nf

@@ -2,9 +2,6 @@ process CELLRANGER_MKGTF {
    tag "$gtf"
    label 'process_low'

-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."


Can we keep an error message when using conda?

maxulysse · 2022-12-13T19:24:58Z

modules/nf-core/cellranger/mkfastq/main.nf

@@ -2,9 +2,6 @@ process CELLRANGER_MKFASTQ {
    tag "mkfastq"
    label 'process_medium'

-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."


Can we keep an error message when using conda?

maxulysse · 2022-12-13T19:25:06Z

modules/nf-core/cellranger/count/main.nf

@@ -2,9 +2,6 @@ process CELLRANGER_COUNT {
    tag "$meta.gem"
    label 'process_high'

-    if (params.enable_conda) {
-        exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."


Can we keep an error message when using conda?

SPPearce · 2022-12-14T08:41:37Z

modules/nf-core/abricate/run/main.nf

@@ -2,7 +2,7 @@ process ABRICATE_RUN {
    tag "$meta.id"
    label 'process_medium'

-    conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
+    conda "bioconda::abricate=1.0.1"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':


Why does this have the URL encoding %3A instead of :? (And another 7 places)

Excellent spot 👀 Not sure but it has happened before and we should probably look for it and remove in any affected modules.

* new module survivor/merge * fix versions * review updates * add stubs * fix tests * changed conda according to #2654 * moved the args to input vals * update meta * update to latest decision * fix test * Update modules/nf-core/survivor/merge/main.nf Co-authored-by: Jonathan Manning <[email protected]> --------- Co-authored-by: Jonathan Manning <[email protected]>

drpatelh added 7 commits December 13, 2022 13:57

Add pinned conda channels

dc0de49

Remove error raise for modules that dont support conda

5d038e8

Add missing conda recipe

6ea938f

Remove error raise for modules that dont support conda

b9f7c1b

Merge branch 'master' of https://github.com/nf-core/modules into conda

606e58c

Bulk change conda syntax across all modules

19a92f4

Bump NF version to >=22.10.1

2c158f9

maxulysse self-requested a review December 13, 2022 20:00

maxulysse approved these changes Dec 13, 2022

View reviewed changes

drpatelh merged commit c8e35eb into nf-core:master Dec 13, 2022

JoseEspinosa mentioned this pull request Dec 13, 2022

new module: jasminesv #2651

Merged

14 tasks

drpatelh mentioned this pull request Dec 13, 2022

Add exit logic for modules that dont support conda #2657

Merged

SPPearce reviewed Dec 14, 2022

View reviewed changes

muffato mentioned this pull request Dec 15, 2022

Minor updates to biscuit modules #2656

Merged

14 tasks

mirpedrol mentioned this pull request Dec 15, 2022

Remove params.enable_conda nf-core/tools#2131

Merged

4 tasks

jemten mentioned this pull request Dec 19, 2022

Update modules to latest version nf-core/raredisease#273

Closed

This was referenced Dec 19, 2022

Configure testing with Podman and Mamba #2675

Closed

Add cd-hit module #2676

Merged

chasemc mentioned this pull request Jan 20, 2023

update nf-core conda format socialgene/sgnf#7

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Bulk change conda syntax for all modules #2654

Bulk change conda syntax for all modules #2654

drpatelh commented Dec 13, 2022

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maxulysse Dec 13, 2022

drpatelh Dec 13, 2022

maxulysse Dec 13, 2022

maxulysse Dec 13, 2022

drpatelh Dec 13, 2022

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maxulysse Dec 13, 2022

maxulysse Dec 13, 2022

maxulysse Dec 13, 2022

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maxulysse Dec 13, 2022

SPPearce Dec 14, 2022 •

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drpatelh Dec 14, 2022

Bulk change conda syntax for all modules #2654

Bulk change conda syntax for all modules #2654

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drpatelh commented Dec 13, 2022

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