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Merged
merged 2 commits into from
Jan 6, 2024
Merged

Molkart local fix #50

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d245f99
Updated molkart-local container version.
FloWuenne Jan 5, 2024
f5abf0d
Added changes to changelog.
FloWuenne Jan 6, 2024
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,12 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.0.1dev - [2024.01.06]

### `Fixed`

- Updated version numbers for all local modules to molkart-local container v0.0.4 due to a bug in version v0.0.3 that prevented the modules to be properly run with singularity.

## v1.0.1dev - [2024.01.04]

### `Added`
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2 changes: 1 addition & 1 deletion modules/local/clahe.nf
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Expand Up @@ -2,7 +2,7 @@ process CLAHE{
tag "$meta.id"
label 'process_medium'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
tuple val(meta), path(image)
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2 changes: 1 addition & 1 deletion modules/local/createanndata.nf
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Expand Up @@ -2,7 +2,7 @@ process CREATE_ANNDATA {
tag "$meta.id"
label 'process_low'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
tuple val(meta), path(spot2cell)
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2 changes: 1 addition & 1 deletion modules/local/createstack.nf
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Expand Up @@ -2,7 +2,7 @@ process CREATE_STACK {
tag "$meta.id"
label 'process_low'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
tuple val(meta), path(image)
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2 changes: 1 addition & 1 deletion modules/local/crophdf5.nf
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Expand Up @@ -2,7 +2,7 @@ process CROPHDF5 {
tag "$meta.id"
label 'process_single'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
tuple val(meta), path(image_stack), val(num_channels)
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2 changes: 1 addition & 1 deletion modules/local/croptiff.nf
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Expand Up @@ -2,7 +2,7 @@ process CROPTIFF {
tag "$meta.id"
label 'process_single'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
tuple val(meta), path(image_stack)
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2 changes: 1 addition & 1 deletion modules/local/maskfilter.nf
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Expand Up @@ -2,7 +2,7 @@ process MASKFILTER {
tag "$meta.id"
label 'process_medium'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
tuple val(meta), path(mask)
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2 changes: 1 addition & 1 deletion modules/local/molkartqc.nf
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Expand Up @@ -2,7 +2,7 @@ process MOLKARTQC{
tag "$meta.id"
label 'process_single'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
tuple val(meta), path(spot_table), path(cellxgene_table), val(segmethod), path(filterqc)
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2 changes: 1 addition & 1 deletion modules/local/molkartqcpng.nf
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@@ -1,7 +1,7 @@
process MOLKARTQCPNG {
label 'process_single'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
path(png)
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2 changes: 1 addition & 1 deletion modules/local/spot2cell.nf
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Expand Up @@ -3,7 +3,7 @@ process SPOT2CELL{
tag "$meta.id"
label 'process_single'

container 'ghcr.io/schapirolabor/molkart-local:v0.0.3'
container 'ghcr.io/schapirolabor/molkart-local:v0.0.4'

input:
tuple val(meta) , path(spot_table)
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2 changes: 1 addition & 1 deletion modules/local/tiffh5convert.nf
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Expand Up @@ -2,7 +2,7 @@ process TIFFH5CONVERT {
tag "$meta.id"
label 'process_single'

container "ghcr.io/schapirolabor/molkart-local:v0.0.3"
container "ghcr.io/schapirolabor/molkart-local:v0.0.4"

input:
tuple val(meta), path(image), val(num_channels)
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