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Build branch main with version main (d8c0c0f)

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Build pipeline: viash-hub.htrnaseq.main-fc9g5

Source commit: d8c0c0f518

Source message: Create umi_length parameter and infer barcode length from sequence (#27)
This commit is contained in:
CI
2025-01-14 09:07:18 +00:00
parent f86c73dccb
commit 37c4f5eb25
61 changed files with 264 additions and 348 deletions
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11
CHANGELOG.md
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@@ -1,9 +1,20 @@
# demultiplex v0.x.x
# New functionality
* Added `umi_length` argument (PR #27).
# Breaking changes
* Removed `wellBarcodesLength` from `parallel_map` workflow (PR #27).
# Minor changes
* Use `v0.3.0` version of cutadapt instead of `main` (PR #23 and PR #24).
* `create_eset`: Update base container image, `R` version and all dependencies
to newer versions (PR #28).
# demultiplex v0.2.0
# New functionality

37
src/eset/create_eset/config.vsh.yaml
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@@ -37,41 +37,18 @@ test_resources:
- path: test_data/mapping_dir
engines:
- type: docker
image: r-base:4.3.0
image: rocker/r2u:24.04
setup:
- type: apt
packages: # most of these are required for devtools
- libcurl4-openssl-dev
- libssl-dev
- libxml2-dev
- libfftw3-dev # Seurat
- libfontconfig1-dev # Seurat
- libfreetype-dev # Seurat
- libhdf5-dev # Seurat
- bzip2 # Seurat
- libharfbuzz-dev # Seurat
- libfribidi-dev # Seurat
- libtiff-dev # Seurat
- libgsl-dev # Seurat
- libcairo-dev # Seurat
- libudunits2-dev # SeuratObject
- procps
- type: r
cran:
- data.table
- BiocManager
- remotes
bioc:
- Biobase
- limma # dependency for nlcv
- a4Core # dependency for nlcv
- MLInterfaces # dependency for nlcv
- multtest # dependency for nlcv
cran:
- nlcv
script: |
remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz", dependencies=TRUE, upgrade_dependencies=FALSE);\
remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz", repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\
bioc:
- Seurat
test_setup:
- type: r
cran:
- testthat
runners:
- type: executable
- type: nextflow

2
src/eset/create_eset/script.R
View File

@@ -217,7 +217,7 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
requireNamespace("Seurat")
seurat_object <- Seurat::CreateSeuratObject(counts = read_matrix)
exprs_matrix <- as.matrix(seurat_object[['RNA']]@counts)
exprs_matrix <- as.matrix(seurat_object[['RNA']]$counts)
# replace "-" with "_" for features with "_"
# before converting to Seurat object
rownames(exprs_matrix)[idx] <- gsub("-", "_", rownames(exprs_matrix)[idx])

4
src/parallel_map/config.vsh.yaml
View File

@@ -35,10 +35,6 @@ argument_groups:
description: The barcodes/wells to process
- name: Barcode arguments
arguments:
- name: "--wellBarcodesLength"
type: integer
required: true
description: The length of the well barcodes
- name: "--umiLength"
type: integer
required: true

28
src/parallel_map/script.sh
View File

@@ -6,7 +6,6 @@ par_input_r2="work/2c/5b8b3a2dd4a988b8838e3f72d38a37/_viash_par/input_r2_1/two__
par_barcodes="ACACCGAATT;GGCTATTGAT"
par_output="./*"
par_genomeDir="star"
par_wellBarcodesLength=10
par_umiLength=10
par_limitBAMsortRAM="10000000000"
meta_cpus=2
@@ -73,16 +72,17 @@ fi
# Define the function that will be used to run a single job
function _run() {
local par_wellBarcodeLength="$1"
local par_UMIlength="$2"
local par_output="$3"
local par_genomeDir="$4"
local par_limitBAMsortRAM="$5"
local par_runThreadN="$6"
local barcode="$7"
local input_R1="$8"
local input_R2="$9"
local par_UMIstart=$(($par_wellBarcodeLength + 1))
local par_UMIlength="$1"
local par_output="$2"
local par_genomeDir="$3"
local par_limitBAMsortRAM="$4"
local par_runThreadN="$5"
local barcode="$6"
local input_R1="$7"
local input_R2="$8"
local barcode_length="${#barcode}"
local umi_start="$(($barcode_length + 1))"
set -eo pipefail
@@ -178,8 +178,8 @@ function _run() {
--outSAMtype BAM SortedByCoordinate \
--soloCBstart 1 \
--readFilesType "Fastx" \
--soloCBlen "$par_wellBarcodeLength" \
--soloUMIstart "$par_UMIstart" \
--soloCBlen "$barcode_length" \
--soloUMIstart "$umi_start" \
--soloUMIlen "$par_UMIlength" \
--soloBarcodeReadLength 0 \
--soloStrand Unstranded \
@@ -235,7 +235,7 @@ parallel_cmd=("parallel" "--jobs" "80%" "--verbose" "--memfree" "2G"
"--joblog" "$par_joblog" "_run" "{}")
# Arguments for which there is one value, so these will not create extra jobs
parallel_cmd+=(":::" "$par_wellBarcodesLength" ":::" "$par_umiLength" ":::" "$par_output" ":::" "$par_genomeDir" ":::" "$par_limitBAMsortRAM" ":::" "$par_runThreadN")
parallel_cmd+=(":::" "$par_umiLength" ":::" "$par_output" ":::" "$par_genomeDir" ":::" "$par_limitBAMsortRAM" ":::" "$par_runThreadN")
# Argument which in fact will cause extra jobs to be spawned, per job one item from each argument will be selected
# Thus, these argument lists should have the same length.

6
src/parallel_map/test.sh
View File

@@ -110,7 +110,6 @@ pushd "$run_1_dir" > /dev/null
--input_r2 "$TMPDIR/sample1_R2.fastq;$TMPDIR/sample2_R2.fastq" \
--genomeDir "$TMPDIR/index/" \
--barcodes "ACAGTCACAG;CGGGTTTACC" \
--wellBarcodesLength 10 \
--umiLength 10 \
--runThreadN 2 \
--output "$TMPDIR/output_*" > /dev/null 2>&1
@@ -203,7 +202,6 @@ pushd "$run_2_dir" > /dev/null
--input_r2 "$TMPDIR/sample1_R2.fastq.gz;$TMPDIR/sample2_R2.fastq.gz" \
--genomeDir "$TMPDIR/index/" \
--barcodes "ACAGTCACAG;CGGGTTTACC" \
--wellBarcodesLength 10 \
--umiLength 10 \
--runThreadN 2 \
--output "$TMPDIR/output_gz_*" > /dev/null 2>&1
@@ -293,7 +291,6 @@ set +eo pipefail
--input_r2 "$TMPDIR/sample1_R2.fastq.gz;$TMPDIR/sample2_R2.fastq.gz" \
--genomeDir "$TMPDIR/index/" \
--barcodes "ACAGTCACAG" \
--wellBarcodesLength 10 \
--umiLength 10 \
--runThreadN 2 \
--output "$TMPDIR/output_gz_*" > /dev/null 2>&1 && echo "Expected non-zero exit code " && exit 1
@@ -310,7 +307,6 @@ set +eo pipefail
--input_r2 "$TMPDIR/sample1_R2.fastq.gz;$TMPDIR/sample2_R2.fastq.gz" \
--genomeDir "$TMPDIR/index/" \
--barcodes "ACAGTCACAG;CGGGTTTACC" \
--wellBarcodesLength 10 \
--umiLength 10 \
--runThreadN 2 \
--output "$TMPDIR/output_run4" > /dev/null 2>&1 && echo "Expected non-zero exit code." && exit 1
@@ -329,7 +325,6 @@ set +eo pipefail
--input_r2 "$TMPDIR/sample1_R2.fastq;$TMPDIR/sample2_R2.fastq" \
--genomeDir "$TMPDIR/index/" \
--barcodes "ACAGTCACAG;CGGGTTTACC" \
--wellBarcodesLength 10 \
--umiLength 10 \
--runThreadN 2 \
--output "$TMPDIR/output_run5_*" > /dev/null 2>&1 && echo "Expected non-zero exit code " && exit 1
@@ -346,7 +341,6 @@ set +eo pipefail
--input_r2 "$TMPDIR/sample1_R2.fastq;$TMPDIR/sample2_R2.fastq" \
--genomeDir "$TMPDIR/index/" \
--barcodes "ACAGTCACAG;CGGGTTTACC" \
--wellBarcodesLength 10 \
--umiLength 10 \
--runThreadN 2 \
--output "$TMPDIR/output_run_6_*" > /dev/null 2>&1 && echo "Expected non-zero exit code " && exit 1

6
src/workflows/htrnaseq/config.vsh.yaml
View File

@@ -23,6 +23,12 @@ argument_groups:
- name: --barcodesFasta
type: file
required: true
- name: "--umi_length"
description: |
Length of the UMI sequences
type: integer
min: 1
default: 10
- name: --genomeDir
type: file
required: true

1
src/workflows/htrnaseq/main.nf
View File

@@ -37,6 +37,7 @@ workflow run_wf {
"input_r1": state.fastq_output_r1[0],
"input_r2": state.fastq_output_r2[0],
"barcode": state.barcode,
"umi_length": state.umi_length,
"pool": state.pool,
"output": state.star_output[0],
"genomeDir": state.genomeDir,

3
src/workflows/parallel_map_wf/config.vsh.yaml
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@@ -22,6 +22,9 @@ argument_groups:
- name: "--barcode"
type: string
required: true
- name: "--umi_length"
type: integer
min: 1
- name: "--pool"
type: string
required: true

3
src/workflows/parallel_map_wf/main.nf
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@@ -25,8 +25,7 @@ workflow run_wf {
"genomeDir": state.genomeDir,
"barcodes": state.wells,
"pool": state.pool,
"wellBarcodesLength": 10,
"umiLength": 10,
"umiLength": state.umi_length,
"output": state.output,
]
},

42
target/executable/eset/create_eset/.config.vsh.yaml
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@@ -170,44 +170,22 @@ runners:
engines:
- type: "docker"
id: "docker"
image: "r-base:4.3.0"
image: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "libcurl4-openssl-dev"
- "libssl-dev"
- "libxml2-dev"
- "libfftw3-dev"
- "libfontconfig1-dev"
- "libfreetype-dev"
- "libhdf5-dev"
- "bzip2"
- "libharfbuzz-dev"
- "libfribidi-dev"
- "libtiff-dev"
- "libgsl-dev"
- "libcairo-dev"
- "libudunits2-dev"
- "procps"
interactive: false
- type: "r"
cran:
- "data.table"
- "nlcv"
bioc:
- "Biobase"
- "limma"
- "a4Core"
- "MLInterfaces"
- "multtest"
script:
- "remotes::install_url(\"https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz\"\
, dependencies=TRUE, upgrade_dependencies=FALSE);\\\nremotes::install_url(\"\
https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz\"\
, repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\\\
\n"
- "Seurat"
bioc_force_install: false
test_setup:
- type: "r"
cran:
- "testthat"
bioc_force_install: false
entrypoint: []
cmd: null
@@ -220,8 +198,8 @@ build_info:
output: "target/executable/eset/create_eset"
executable: "target/executable/eset/create_eset/create_eset"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

23
target/executable/eset/create_eset/create_eset
View File

@@ -468,29 +468,18 @@ function ViashDockerfile {
if [[ "$engine_id" == "docker" ]]; then
cat << 'VIASHDOCKER'
FROM r-base:4.3.0
FROM rocker/r2u:24.04
ENTRYPOINT []
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libfftw3-dev libfontconfig1-dev libfreetype-dev libhdf5-dev bzip2 libharfbuzz-dev libfribidi-dev libtiff-dev libgsl-dev libcairo-dev libudunits2-dev procps && \
rm -rf /var/lib/apt/lists/*
RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
Rscript -e 'if (!requireNamespace("Biobase", quietly = TRUE)) BiocManager::install("Biobase")' && \
Rscript -e 'if (!requireNamespace("limma", quietly = TRUE)) BiocManager::install("limma")' && \
Rscript -e 'if (!requireNamespace("a4Core", quietly = TRUE)) BiocManager::install("a4Core")' && \
Rscript -e 'if (!requireNamespace("MLInterfaces", quietly = TRUE)) BiocManager::install("MLInterfaces")' && \
Rscript -e 'if (!requireNamespace("multtest", quietly = TRUE)) BiocManager::install("multtest")' && \
Rscript -e 'remotes::install_cran(c("nlcv"), repos = "https://cran.rstudio.com")' && \
Rscript -e 'remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz", dependencies=TRUE, upgrade_dependencies=FALSE);\
remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz", repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\
'
Rscript -e 'if (!requireNamespace("Seurat", quietly = TRUE)) BiocManager::install("Seurat")' && \
Rscript -e 'remotes::install_cran(c("data.table", "nlcv"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
LABEL org.opencontainers.image.created="2025-01-10T15:09:09Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -1362,7 +1351,7 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
requireNamespace("Seurat")
seurat_object <- Seurat::CreateSeuratObject(counts = read_matrix)
exprs_matrix <- as.matrix(seurat_object[['RNA']]@counts)
exprs_matrix <- as.matrix(seurat_object[['RNA']]\$counts)
# replace "-" with "_" for features with "_"
# before converting to Seurat object
rownames(exprs_matrix)[idx] <- gsub("-", "_", rownames(exprs_matrix)[idx])

4
target/executable/eset/create_fdata/.config.vsh.yaml
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@@ -177,8 +177,8 @@ build_info:
output: "target/executable/eset/create_fdata"
executable: "target/executable/eset/create_fdata/create_fdata"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/eset/create_fdata/create_fdata
View File

@@ -478,9 +478,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
LABEL org.opencontainers.image.created="2025-01-10T15:09:10Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/eset/create_pdata/.config.vsh.yaml
View File

@@ -191,8 +191,8 @@ build_info:
output: "target/executable/eset/create_pdata"
executable: "target/executable/eset/create_pdata/create_pdata"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/eset/create_pdata/create_pdata
View File

@@ -488,9 +488,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
LABEL org.opencontainers.image.created="2025-01-10T15:09:08Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -148,8 +148,8 @@ build_info:
output: "target/executable/integration_test_components/htrnaseq/check_eset"
executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/integration_test_components/htrnaseq/check_eset/check_eset
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@@ -470,9 +470,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
LABEL org.opencontainers.image.created="2025-01-10T15:09:10Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -158,8 +158,8 @@ build_info:
output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
View File

@@ -476,9 +476,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
LABEL org.opencontainers.image.created="2025-01-10T15:09:10Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

12
target/executable/parallel_map/.config.vsh.yaml
View File

@@ -68,14 +68,6 @@ argument_groups:
multiple_sep: ";"
- name: "Barcode arguments"
arguments:
- type: "integer"
name: "--wellBarcodesLength"
description: "The length of the well barcodes"
info: null
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--umiLength"
description: "The length of the UMIs"
@@ -264,8 +256,8 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

57
target/executable/parallel_map/parallel_map
View File

@@ -197,10 +197,6 @@ function ViashHelp {
echo " The barcodes/wells to process"
echo ""
echo "Barcode arguments:"
echo " --wellBarcodesLength"
echo " type: integer, required parameter"
echo " The length of the well barcodes"
echo ""
echo " --umiLength"
echo " type: integer, required parameter"
echo " The length of the UMIs"
@@ -517,9 +513,9 @@ ENV STAR_BINARY=STAR
COPY STAR /usr/local/bin/$STAR_BINARY
LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
LABEL org.opencontainers.image.created="2025-01-10T15:09:09Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:10Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -721,17 +717,6 @@ while [[ $# -gt 0 ]]; do
fi
shift 1
;;
--wellBarcodesLength)
[ -n "$VIASH_PAR_WELLBARCODESLENGTH" ] && ViashError Bad arguments for option \'--wellBarcodesLength\': \'$VIASH_PAR_WELLBARCODESLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_WELLBARCODESLENGTH="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --wellBarcodesLength. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--wellBarcodesLength=*)
[ -n "$VIASH_PAR_WELLBARCODESLENGTH" ] && ViashError Bad arguments for option \'--wellBarcodesLength=*\': \'$VIASH_PAR_WELLBARCODESLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_WELLBARCODESLENGTH=$(ViashRemoveFlags "$1")
shift 1
;;
--umiLength)
[ -n "$VIASH_PAR_UMILENGTH" ] && ViashError Bad arguments for option \'--umiLength\': \'$VIASH_PAR_UMILENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UMILENGTH="$2"
@@ -975,10 +960,6 @@ if [ -z ${VIASH_PAR_BARCODES+x} ]; then
ViashError '--barcodes' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_WELLBARCODESLENGTH+x} ]; then
ViashError '--wellBarcodesLength' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_UMILENGTH+x} ]; then
ViashError '--umiLength' is a required argument. Use "--help" to get more information on the parameters.
exit 1
@@ -1054,12 +1035,6 @@ if [ ! -z "$VIASH_PAR_GENOMEDIR" ] && [ ! -e "$VIASH_PAR_GENOMEDIR" ]; then
fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_WELLBARCODESLENGTH" ]]; then
if ! [[ "$VIASH_PAR_WELLBARCODESLENGTH" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--wellBarcodesLength' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_UMILENGTH" ]]; then
if ! [[ "$VIASH_PAR_UMILENGTH" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--umiLength' has to be an integer. Use "--help" to get more information on the parameters.
@@ -1289,7 +1264,6 @@ $( if [ ! -z ${VIASH_PAR_INPUT_R1+x} ]; then echo "${VIASH_PAR_INPUT_R1}" | sed
$( if [ ! -z ${VIASH_PAR_INPUT_R2+x} ]; then echo "${VIASH_PAR_INPUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_input_r2='&'#" ; else echo "# par_input_r2="; fi )
$( if [ ! -z ${VIASH_PAR_GENOMEDIR+x} ]; then echo "${VIASH_PAR_GENOMEDIR}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeDir='&'#" ; else echo "# par_genomeDir="; fi )
$( if [ ! -z ${VIASH_PAR_BARCODES+x} ]; then echo "${VIASH_PAR_BARCODES}" | sed "s#'#'\"'\"'#g;s#.*#par_barcodes='&'#" ; else echo "# par_barcodes="; fi )
$( if [ ! -z ${VIASH_PAR_WELLBARCODESLENGTH+x} ]; then echo "${VIASH_PAR_WELLBARCODESLENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_wellBarcodesLength='&'#" ; else echo "# par_wellBarcodesLength="; fi )
$( if [ ! -z ${VIASH_PAR_UMILENGTH+x} ]; then echo "${VIASH_PAR_UMILENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_umiLength='&'#" ; else echo "# par_umiLength="; fi )
$( if [ ! -z ${VIASH_PAR_LIMITBAMSORTRAM+x} ]; then echo "${VIASH_PAR_LIMITBAMSORTRAM}" | sed "s#'#'\"'\"'#g;s#.*#par_limitBAMsortRAM='&'#" ; else echo "# par_limitBAMsortRAM="; fi )
$( if [ ! -z ${VIASH_PAR_RUNTHREADN+x} ]; then echo "${VIASH_PAR_RUNTHREADN}" | sed "s#'#'\"'\"'#g;s#.*#par_runThreadN='&'#" ; else echo "# par_runThreadN="; fi )
@@ -1376,16 +1350,17 @@ fi
# Define the function that will be used to run a single job
function _run() {
local par_wellBarcodeLength="\$1"
local par_UMIlength="\$2"
local par_output="\$3"
local par_genomeDir="\$4"
local par_limitBAMsortRAM="\$5"
local par_runThreadN="\$6"
local barcode="\$7"
local input_R1="\$8"
local input_R2="\$9"
local par_UMIstart=\$((\$par_wellBarcodeLength + 1))
local par_UMIlength="\$1"
local par_output="\$2"
local par_genomeDir="\$3"
local par_limitBAMsortRAM="\$4"
local par_runThreadN="\$5"
local barcode="\$6"
local input_R1="\$7"
local input_R2="\$8"
local barcode_length="\${#barcode}"
local umi_start="\$((\$barcode_length + 1))"
set -eo pipefail
@@ -1481,8 +1456,8 @@ function _run() {
--outSAMtype BAM SortedByCoordinate \\
--soloCBstart 1 \\
--readFilesType "Fastx" \\
--soloCBlen "\$par_wellBarcodeLength" \\
--soloUMIstart "\$par_UMIstart" \\
--soloCBlen "\$barcode_length" \\
--soloUMIstart "\$umi_start" \\
--soloUMIlen "\$par_UMIlength" \\
--soloBarcodeReadLength 0 \\
--soloStrand Unstranded \\
@@ -1538,7 +1513,7 @@ parallel_cmd=("parallel" "--jobs" "80%" "--verbose" "--memfree" "2G"
"--joblog" "\$par_joblog" "_run" "{}")
# Arguments for which there is one value, so these will not create extra jobs
parallel_cmd+=(":::" "\$par_wellBarcodesLength" ":::" "\$par_umiLength" ":::" "\$par_output" ":::" "\$par_genomeDir" ":::" "\$par_limitBAMsortRAM" ":::" "\$par_runThreadN")
parallel_cmd+=(":::" "\$par_umiLength" ":::" "\$par_output" ":::" "\$par_genomeDir" ":::" "\$par_limitBAMsortRAM" ":::" "\$par_runThreadN")
# Argument which in fact will cause extra jobs to be spawned, per job one item from each argument will be selected
# Thus, these argument lists should have the same length.

4
target/executable/report/create_report/.config.vsh.yaml
View File

@@ -201,8 +201,8 @@ build_info:
output: "target/executable/report/create_report"
executable: "target/executable/report/create_report/create_report"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/report/create_report/create_report
View File

@@ -476,9 +476,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component report create_report"
LABEL org.opencontainers.image.created="2025-01-10T15:09:09Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/stats/combine_star_logs"
executable: "target/executable/stats/combine_star_logs/combine_star_logs"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/stats/combine_star_logs/combine_star_logs
View File

@@ -490,9 +490,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
LABEL org.opencontainers.image.created="2025-01-10T15:09:09Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -182,8 +182,8 @@ build_info:
output: "target/executable/stats/generate_pool_statistics"
executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/stats/generate_pool_statistics/generate_pool_statistics
View File

@@ -483,9 +483,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
LABEL org.opencontainers.image.created="2025-01-10T15:09:08Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -262,8 +262,8 @@ build_info:
output: "target/executable/stats/generate_well_statistics"
executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/executable/stats/generate_well_statistics/generate_well_statistics
View File

@@ -520,9 +520,9 @@ RUN pip install --upgrade pip && \
LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
LABEL org.opencontainers.image.created="2025-01-10T15:09:09Z"
LABEL org.opencontainers.image.created="2025-01-14T07:38:12Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

42
target/nextflow/eset/create_eset/.config.vsh.yaml
View File

@@ -170,44 +170,22 @@ runners:
engines:
- type: "docker"
id: "docker"
image: "r-base:4.3.0"
image: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "libcurl4-openssl-dev"
- "libssl-dev"
- "libxml2-dev"
- "libfftw3-dev"
- "libfontconfig1-dev"
- "libfreetype-dev"
- "libhdf5-dev"
- "bzip2"
- "libharfbuzz-dev"
- "libfribidi-dev"
- "libtiff-dev"
- "libgsl-dev"
- "libcairo-dev"
- "libudunits2-dev"
- "procps"
interactive: false
- type: "r"
cran:
- "data.table"
- "nlcv"
bioc:
- "Biobase"
- "limma"
- "a4Core"
- "MLInterfaces"
- "multtest"
script:
- "remotes::install_url(\"https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz\"\
, dependencies=TRUE, upgrade_dependencies=FALSE);\\\nremotes::install_url(\"\
https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz\"\
, repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\\\
\n"
- "Seurat"
bioc_force_install: false
test_setup:
- type: "r"
cran:
- "testthat"
bioc_force_install: false
entrypoint: []
cmd: null
@@ -220,8 +198,8 @@ build_info:
output: "target/nextflow/eset/create_eset"
executable: "target/nextflow/eset/create_eset/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

46
target/nextflow/eset/create_eset/main.nf
View File

@@ -3034,46 +3034,28 @@ meta = [
{
"type" : "docker",
"id" : "docker",
"image" : "r-base:4.3.0",
"image" : "rocker/r2u:24.04",
"target_registry" : "images.viash-hub.com",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
"type" : "apt",
"packages" : [
"libcurl4-openssl-dev",
"libssl-dev",
"libxml2-dev",
"libfftw3-dev",
"libfontconfig1-dev",
"libfreetype-dev",
"libhdf5-dev",
"bzip2",
"libharfbuzz-dev",
"libfribidi-dev",
"libtiff-dev",
"libgsl-dev",
"libcairo-dev",
"libudunits2-dev",
"procps"
],
"interactive" : false
},
{
"type" : "r",
"cran" : [
"data.table",
"nlcv"
],
"bioc" : [
"Biobase",
"limma",
"a4Core",
"MLInterfaces",
"multtest"
"Seurat"
],
"script" : [
"remotes::install_url(\\"https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz\\", dependencies=TRUE, upgrade_dependencies=FALSE);\\\\\nremotes::install_url(\\"https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz\\", repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\\\\\n"
"bioc_force_install" : false
}
],
"test_setup" : [
{
"type" : "r",
"cran" : [
"testthat"
],
"bioc_force_install" : false
}
@@ -3090,8 +3072,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_eset",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3391,7 +3373,7 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
requireNamespace("Seurat")
seurat_object <- Seurat::CreateSeuratObject(counts = read_matrix)
exprs_matrix <- as.matrix(seurat_object[['RNA']]@counts)
exprs_matrix <- as.matrix(seurat_object[['RNA']]\\$counts)
# replace "-" with "_" for features with "_"
# before converting to Seurat object
rownames(exprs_matrix)[idx] <- gsub("-", "_", rownames(exprs_matrix)[idx])

4
target/nextflow/eset/create_fdata/.config.vsh.yaml
View File

@@ -177,8 +177,8 @@ build_info:
output: "target/nextflow/eset/create_fdata"
executable: "target/nextflow/eset/create_fdata/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/eset/create_fdata/main.nf
View File

@@ -3044,8 +3044,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_fdata",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/eset/create_pdata/.config.vsh.yaml
View File

@@ -191,8 +191,8 @@ build_info:
output: "target/nextflow/eset/create_pdata"
executable: "target/nextflow/eset/create_pdata/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/eset/create_pdata/main.nf
View File

@@ -3058,8 +3058,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/eset/create_pdata",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
View File

@@ -148,8 +148,8 @@ build_info:
output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
View File

@@ -2997,8 +2997,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
View File

@@ -158,8 +158,8 @@ build_info:
output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
View File

@@ -3009,8 +3009,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

12
target/nextflow/parallel_map/.config.vsh.yaml
View File

@@ -68,14 +68,6 @@ argument_groups:
multiple_sep: ";"
- name: "Barcode arguments"
arguments:
- type: "integer"
name: "--wellBarcodesLength"
description: "The length of the well barcodes"
info: null
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--umiLength"
description: "The length of the UMIs"
@@ -264,8 +256,8 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

41
target/nextflow/parallel_map/main.nf
View File

@@ -2903,15 +2903,6 @@ meta = [
{
"name" : "Barcode arguments",
"arguments" : [
{
"type" : "integer",
"name" : "--wellBarcodesLength",
"description" : "The length of the well barcodes",
"required" : true,
"direction" : "input",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "integer",
"name" : "--umiLength",
@@ -3148,8 +3139,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3207,7 +3198,6 @@ $( if [ ! -z ${VIASH_PAR_INPUT_R1+x} ]; then echo "${VIASH_PAR_INPUT_R1}" | sed
$( if [ ! -z ${VIASH_PAR_INPUT_R2+x} ]; then echo "${VIASH_PAR_INPUT_R2}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_r2='&'#" ; else echo "# par_input_r2="; fi )
$( if [ ! -z ${VIASH_PAR_GENOMEDIR+x} ]; then echo "${VIASH_PAR_GENOMEDIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_genomeDir='&'#" ; else echo "# par_genomeDir="; fi )
$( if [ ! -z ${VIASH_PAR_BARCODES+x} ]; then echo "${VIASH_PAR_BARCODES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_barcodes='&'#" ; else echo "# par_barcodes="; fi )
$( if [ ! -z ${VIASH_PAR_WELLBARCODESLENGTH+x} ]; then echo "${VIASH_PAR_WELLBARCODESLENGTH}" | sed "s#'#'\\"'\\"'#g;s#.*#par_wellBarcodesLength='&'#" ; else echo "# par_wellBarcodesLength="; fi )
$( if [ ! -z ${VIASH_PAR_UMILENGTH+x} ]; then echo "${VIASH_PAR_UMILENGTH}" | sed "s#'#'\\"'\\"'#g;s#.*#par_umiLength='&'#" ; else echo "# par_umiLength="; fi )
$( if [ ! -z ${VIASH_PAR_LIMITBAMSORTRAM+x} ]; then echo "${VIASH_PAR_LIMITBAMSORTRAM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_limitBAMsortRAM='&'#" ; else echo "# par_limitBAMsortRAM="; fi )
$( if [ ! -z ${VIASH_PAR_RUNTHREADN+x} ]; then echo "${VIASH_PAR_RUNTHREADN}" | sed "s#'#'\\"'\\"'#g;s#.*#par_runThreadN='&'#" ; else echo "# par_runThreadN="; fi )
@@ -3294,16 +3284,17 @@ fi
# Define the function that will be used to run a single job
function _run() {
local par_wellBarcodeLength="\\$1"
local par_UMIlength="\\$2"
local par_output="\\$3"
local par_genomeDir="\\$4"
local par_limitBAMsortRAM="\\$5"
local par_runThreadN="\\$6"
local barcode="\\$7"
local input_R1="\\$8"
local input_R2="\\$9"
local par_UMIstart=\\$((\\$par_wellBarcodeLength + 1))
local par_UMIlength="\\$1"
local par_output="\\$2"
local par_genomeDir="\\$3"
local par_limitBAMsortRAM="\\$4"
local par_runThreadN="\\$5"
local barcode="\\$6"
local input_R1="\\$7"
local input_R2="\\$8"
local barcode_length="\\${#barcode}"
local umi_start="\\$((\\$barcode_length + 1))"
set -eo pipefail
@@ -3399,8 +3390,8 @@ function _run() {
--outSAMtype BAM SortedByCoordinate \\\\
--soloCBstart 1 \\\\
--readFilesType "Fastx" \\\\
--soloCBlen "\\$par_wellBarcodeLength" \\\\
--soloUMIstart "\\$par_UMIstart" \\\\
--soloCBlen "\\$barcode_length" \\\\
--soloUMIstart "\\$umi_start" \\\\
--soloUMIlen "\\$par_UMIlength" \\\\
--soloBarcodeReadLength 0 \\\\
--soloStrand Unstranded \\\\
@@ -3456,7 +3447,7 @@ parallel_cmd=("parallel" "--jobs" "80%" "--verbose" "--memfree" "2G"
"--joblog" "\\$par_joblog" "_run" "{}")
# Arguments for which there is one value, so these will not create extra jobs
parallel_cmd+=(":::" "\\$par_wellBarcodesLength" ":::" "\\$par_umiLength" ":::" "\\$par_output" ":::" "\\$par_genomeDir" ":::" "\\$par_limitBAMsortRAM" ":::" "\\$par_runThreadN")
parallel_cmd+=(":::" "\\$par_umiLength" ":::" "\\$par_output" ":::" "\\$par_genomeDir" ":::" "\\$par_limitBAMsortRAM" ":::" "\\$par_runThreadN")
# Argument which in fact will cause extra jobs to be spawned, per job one item from each argument will be selected
# Thus, these argument lists should have the same length.

10
target/nextflow/parallel_map/nextflow_schema.json
View File

@@ -64,16 +64,6 @@
"properties": {
"wellBarcodesLength": {
"type":
"integer",
"description": "Type: `integer`, required. The length of the well barcodes",
"help_text": "Type: `integer`, required. The length of the well barcodes"
}
,
"umiLength": {
"type":
"integer",

4
target/nextflow/report/create_report/.config.vsh.yaml
View File

@@ -201,8 +201,8 @@ build_info:
output: "target/nextflow/report/create_report"
executable: "target/nextflow/report/create_report/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/report/create_report/main.nf
View File

@@ -3077,8 +3077,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/report/create_report",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/combine_star_logs/.config.vsh.yaml
View File

@@ -198,8 +198,8 @@ build_info:
output: "target/nextflow/stats/combine_star_logs"
executable: "target/nextflow/stats/combine_star_logs/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/stats/combine_star_logs/main.nf
View File

@@ -3060,8 +3060,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/combine_star_logs",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
View File

@@ -182,8 +182,8 @@ build_info:
output: "target/nextflow/stats/generate_pool_statistics"
executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/stats/generate_pool_statistics/main.nf
View File

@@ -3044,8 +3044,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_pool_statistics",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
View File

@@ -262,8 +262,8 @@ build_info:
output: "target/nextflow/stats/generate_well_statistics"
executable: "target/nextflow/stats/generate_well_statistics/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/stats/generate_well_statistics/main.nf
View File

@@ -3135,8 +3135,8 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/stats/generate_well_statistics",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

15
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
View File

@@ -51,6 +51,17 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--umi_length"
description: "Length of the UMI sequences\n"
info: null
default:
- 10
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--genomeDir"
info: null
@@ -308,8 +319,8 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/stats/combine_star_logs"
- "target/nextflow/stats/generate_pool_statistics"

18
target/nextflow/workflows/htrnaseq/main.nf
View File

@@ -2869,6 +2869,19 @@ meta = [
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "integer",
"name" : "--umi_length",
"description" : "Length of the UMI sequences\n",
"default" : [
10
],
"required" : false,
"min" : 1,
"direction" : "input",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "file",
"name" : "--genomeDir",
@@ -3210,8 +3223,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3306,6 +3319,7 @@ workflow run_wf {
"input_r1": state.fastq_output_r1[0],
"input_r2": state.fastq_output_r2[0],
"barcode": state.barcode,
"umi_length": state.umi_length,
"pool": state.pool,
"output": state.star_output[0],
"genomeDir": state.genomeDir,

11
target/nextflow/workflows/htrnaseq/nextflow_schema.json
View File

@@ -43,6 +43,17 @@
}
,
"umi_length": {
"type":
"integer",
"description": "Type: `integer`, default: `10`. Length of the UMI sequences\n",
"help_text": "Type: `integer`, default: `10`. Length of the UMI sequences\n"
,
"default":10
}
,
"genomeDir": {
"type":

12
target/nextflow/workflows/parallel_map_wf/.config.vsh.yaml
View File

@@ -43,6 +43,14 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--umi_length"
info: null
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--pool"
info: null
@@ -175,8 +183,8 @@ build_info:
output: "target/nextflow/workflows/parallel_map_wf"
executable: "target/nextflow/workflows/parallel_map_wf/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/parallel_map"
- "target/nextflow/workflows/utils/groupWells"

16
target/nextflow/workflows/parallel_map_wf/main.nf
View File

@@ -2865,6 +2865,15 @@ meta = [
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "integer",
"name" : "--umi_length",
"required" : false,
"min" : 1,
"direction" : "input",
"multiple" : false,
"multiple_sep" : ";"
},
{
"type" : "string",
"name" : "--pool",
@@ -3028,8 +3037,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/parallel_map_wf",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",
@@ -3104,8 +3113,7 @@ workflow run_wf {
"genomeDir": state.genomeDir,
"barcodes": state.wells,
"pool": state.pool,
"wellBarcodesLength": 10,
"umiLength": 10,
"umiLength": state.umi_length,
"output": state.output,
]
},

10
target/nextflow/workflows/parallel_map_wf/nextflow_schema.json
View File

@@ -43,6 +43,16 @@
}
,
"umi_length": {
"type":
"integer",
"description": "Type: `integer`. ",
"help_text": "Type: `integer`. "
}
,
"pool": {
"type":

4
target/nextflow/workflows/utils/groupWells/.config.vsh.yaml
View File

@@ -185,8 +185,8 @@ build_info:
output: "target/nextflow/workflows/utils/groupWells"
executable: "target/nextflow/workflows/utils/groupWells/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"
version: "main"

4
target/nextflow/workflows/utils/groupWells/main.nf
View File

@@ -3039,8 +3039,8 @@ meta = [
"engine" : "native",
"output" : "target/nextflow/workflows/utils/groupWells",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",

4
target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
View File

@@ -255,8 +255,8 @@ build_info:
output: "target/nextflow/workflows/well_demultiplex"
executable: "target/nextflow/workflows/well_demultiplex/main.nf"
viash_version: "0.9.0"
git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
- "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"

4
target/nextflow/workflows/well_demultiplex/main.nf
View File

@@ -3134,8 +3134,8 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_demultiplex",
"viash_version" : "0.9.0",
"git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
"git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
"git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
"git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
},
"package_config" : {
"name" : "htrnaseq",