Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Move conda-checks (first batch) #3686

Merged
merged 6 commits into from
Aug 2, 2023
Merged

Move conda-checks (first batch) #3686

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
1711cb5
Moving conda-check and replacing exit 1 with error-cmd
asp8200 Aug 1, 2023
b17835c
Adding conda-check in stub-section
asp8200 Aug 1, 2023
c332c41
Adding conda-check in stub-section
asp8200 Aug 1, 2023
7894651
Merge branch 'master' into move_conda_check
asp8200 Aug 1, 2023
101f14d
Updating certain md5sums. Ok by Emiller88. Related to https://github.…
asp8200 Aug 1, 2023
026eaac
Switching from exit 1 to error-cmd and correcting error-msg
asp8200 Aug 1, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 4 additions & 5 deletions modules/nf-core/bases2fastq/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,6 @@ process BASES2FASTQ {

container "nf-core/bases2fastq:1.1.0"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "BASES2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}

input:
tuple val(meta), path(run_manifest), path(run_dir)

Expand All @@ -26,6 +21,10 @@ process BASES2FASTQ {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BASES2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def runManifest = run_manifest ? "-r ${run_manifest}" : ""
Expand Down
13 changes: 8 additions & 5 deletions modules/nf-core/basicpy/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,6 @@ process BASICPY {
tag "$meta.id"
label 'process_single'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "Basicpy module does not support Conda. Please use Docker / Singularity instead."
}

container "docker.io/yfukai/basicpy-docker-mcmicro:0.2.1"

input:
Expand All @@ -20,6 +15,10 @@ process BASICPY {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = "1.0.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping
Expand All @@ -33,6 +32,10 @@ process BASICPY {
"""

stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "Basicpy module does not support Conda. Please use Docker / Singularity instead."
}
"""
touch ${prefix}.-dfp.tiff
touch ${prefix}.-dfp.tiff
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/bcl2fastq/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,6 @@ process BCL2FASTQ {

container "nf-core/bcl2fastq:2.20.0.422"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "BCL2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}

input:
tuple val(meta), path(samplesheet), path(run_dir)

Expand All @@ -26,6 +21,10 @@ process BCL2FASTQ {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BCL2FASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/bclconvert/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,6 @@ process BCLCONVERT {

container "nf-core/bclconvert:4.0.3"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "BCLCONVERT module does not support Conda. Please use Docker / Singularity / Podman instead."
}

input:
tuple val(meta), path(samplesheet), path(run_dir)

Expand All @@ -26,6 +21,10 @@ process BCLCONVERT {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "BCLCONVERT module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
Expand Down
12 changes: 8 additions & 4 deletions modules/nf-core/cellpose/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,6 @@ process CELLPOSE {
tag "$meta.id"
label 'process_medium'

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."}

container "docker.io/biocontainers/cellpose:2.1.1_cv2"

input:
Expand All @@ -20,6 +16,10 @@ process CELLPOSE {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def model_command = model ? "--pretrained_model $model" : ""
Expand All @@ -38,6 +38,10 @@ process CELLPOSE {
END_VERSIONS
"""
stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead."
}
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = "2.1.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
Expand Down
13 changes: 8 additions & 5 deletions modules/nf-core/cellranger/count/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,6 @@ process CELLRANGER_COUNT {

container "nf-core/cellranger:7.1.0"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
}

input:
tuple val(meta), path(reads, stageAs: "fastq_???/*")
path reference
Expand All @@ -21,11 +16,19 @@ process CELLRANGER_COUNT {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
}
args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
template "cellranger_count.py"

stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "CELLRANGER_COUNT module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir -p "${prefix}/outs/"
Expand Down
13 changes: 8 additions & 5 deletions modules/nf-core/cellranger/mkfastq/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,6 @@ process CELLRANGER_MKFASTQ {

container "docker.io/nfcore/cellrangermkfastq:7.1.0"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}

input:
path bcl
path csv
Expand All @@ -21,6 +16,10 @@ process CELLRANGER_MKFASTQ {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${bcl.getSimpleName()}"
"""
Expand All @@ -38,6 +37,10 @@ process CELLRANGER_MKFASTQ {
"""

stub:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "CELLRANGER_MKFASTQ module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def prefix = task.ext.prefix ?: "${bcl.getSimpleName()}"
"""
mkdir -p "${prefix}/outs/fastq_path/"
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/cellranger/mkgtf/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,6 @@ process CELLRANGER_MKGTF {

container "nf-core/cellranger:7.1.0"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "CELLRANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
}

input:
path gtf

Expand All @@ -20,6 +15,10 @@ process CELLRANGER_MKGTF {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "CELLRANGER_MKGTF module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${gtf.baseName}.filtered"
"""
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/cellranger/mkref/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,6 @@ process CELLRANGER_MKREF {

container "nf-core/cellranger:7.1.0"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
}

input:
path fasta
path gtf
Expand All @@ -22,6 +17,10 @@ process CELLRANGER_MKREF {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
"""
cellranger \\
Expand Down
9 changes: 4 additions & 5 deletions modules/nf-core/cellranger/mkvdjref/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,6 @@ process CELLRANGER_MKVDJREF {

container "nf-core/cellranger:7.1.0"

// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
exit 1, "CELLRANGER_MKREF module does not support Conda. Please use Docker / Singularity / Podman instead."
}

input:
path fasta
path gtf
Expand All @@ -22,6 +17,10 @@ process CELLRANGER_MKVDJREF {
task.ext.when == null || task.ext.when

script:
// Exit if running this module with -profile conda / -profile mamba
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
error "CELLRANGER_MKVDJREF module does not support Conda. Please use Docker / Singularity / Podman instead."
}
def args = task.ext.args ?: ''
"""
cellranger \\
Expand Down
6 changes: 3 additions & 3 deletions tests/modules/nf-core/bases2fastq/test.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@
files:
- path: output/bases2fastq/output/Bases2Fastq-Sim_QC.html
- path: output/bases2fastq/output/Metrics.csv
md5sum: 0ec6da2b82e191098283474356024abf
md5sum: a8094b308b5653071ac029a27733e4a6
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

why do the checksums change if no version change was done?

Copy link
Contributor Author

@asp8200 asp8200 Aug 1, 2023 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Fair question. I got the impression from @emiller88 that it has something to do with this ongoing PR. (Perhaps some test-data was updated?) I asked Edmund whether I should update the md5sums, and he agreed, and so I did, and the tests worked :-)

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I still don't understand how this got into master if the md5sums were failing- unless someone merged a failing PR somewhere.

Copy link
Member

@pinin4fjords pinin4fjords Aug 1, 2023 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ahh, you think test data, sorry, makes sense

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Lots of PRs have been merged with failing tests, one was merged yesterday. Check out this PR with an attempt to fix it: #3679

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

As-is it at least seems possible with our current mechanisms that changes to test data could do this though. We should close that loophole even if it's not actually the culprit here.

- path: output/bases2fastq/output/RunManifest.json
md5sum: a07dce8ee25c2a6f9355b677c26b53e2
- path: output/bases2fastq/output/RunStats.json
- path: output/bases2fastq/output/UnassignedSequences.csv
md5sum: 11c1693830ce941b8cfb8d2431a59097
- path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R1.fastq.gz
md5sum: 218abc70f61e8e8199a68f83ae836184
md5sum: 831c90ea31eff881e825cda691da77ae
- path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_R2.fastq.gz
md5sum: b95109bfb204daa150b61239d3368ee2
md5sum: e6c1f7ec00910ef195ff3d427c7a9f23
- path: output/bases2fastq/output/Samples/DefaultSample/DefaultSample_stats.json
Loading