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Build branch main_pipeline with version main_pipeline (bdd7091)

Browse Source 
Build pipeline: viash-hub.htrnaseq.main-pipeline-ls5l5

Source commit: bdd7091d5b

Source message: Fix params.yaml and update integration_test
This commit is contained in:
CI
2024-08-20 15:32:30 +00:00
parent 8aa5e10929
commit 15cd1e1fa3
20 changed files with 247 additions and 30 deletions
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20
README.md
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@@ -9,15 +9,15 @@ The pipeline can be run by creating a `params.yaml` file like this:
```yaml
param_list:
- input_r1: "test_resources/100k/SRR14730301/VH02001612_S9_R1_001.fastq"
input_r2: "test_resources/100k/SRR14730301/VH02001612_S9_R2_001.fastq"
genomeDir: "test_resources/genomeDir/gencode.v41.star.sparse"
barcodesFasta: "test_resources/2-wells.fasta"
- input_r1: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R1_001.fastq"
input_r2: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R2_001.fastq"
genomeDir: "gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.star.sparse"
barcodesFasta: "gs://viash-hub-test-data/htrnaseq/v1/2-wells.fasta"
id: sample_one
- input_r1: "test_resources/100k/SRR14730302/VH02001614_S8_R1_001.fastq"
input_r2: "test_resources/100k/SRR14730302/VH02001614_S8_R2_001.fastq"
genomeDir: "test_resources/genomeDir/gencode.v41.star.sparse"
barcodesFasta: "test_resources/2-wells.fasta"
- input_r1: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730302/VH02001614_S8_R1_001.fastq"
input_r2: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730302/VH02001614_S8_R2_001.fastq"
genomeDir: "gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.star.sparse"
barcodesFasta: "gs://viash-hub-test-data/htrnaseq/v1/2-wells.fasta"
id: sample_two
```
@@ -29,8 +29,8 @@ nextflow run . -main-script target/nextflow/workflows/htrnaseq/main.nf \
-profile docker \
-c target/nextflow/workflows/htrnaseq/nextflow.config \
-params-file params.yaml \
-publish_dir output \
-resume
-resume \
--publish_dir output
```
Or, by running `src/workflows/htrnaseq/integration_test.sh`.

6
src/workflows/htrnaseq/integration_test.sh
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@@ -7,13 +7,13 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
cd "$REPO_ROOT"
# Make sure the workflow is built
viash ns build -q 'workflows|parallel_map'
viash ns build --setup cb
export NXF_VER=24.04.3
export NXF_VER=24.04.4
nextflow run . \
-main-script target/nextflow/workflows/htrnaseq/main.nf \
-params-file params.yaml \
-params-file ./src/workflows/htrnaseq/params.yaml \
-config ./src/config/tests.config \
-profile docker \
--publish_dir output \

11
src/workflows/htrnaseq/params.yaml Normal file
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@@ -0,0 +1,11 @@
param_list:
- input_r1: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R1_001.fastq"
input_r2: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730301/VH02001612_S9_R2_001.fastq"
genomeDir: "gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.star.sparse"
barcodesFasta: "gs://viash-hub-test-data/htrnaseq/v1/2-wells.fasta"
id: sample_one
- input_r1: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730302/VH02001614_S8_R1_001.fastq"
input_r2: "gs://viash-hub-test-data/htrnaseq/v1/100k/SRR14730302/VH02001614_S8_R2_001.fastq"
genomeDir: "gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.star.sparse"
barcodesFasta: "gs://viash-hub-test-data/htrnaseq/v1/2-wells.fasta"
id: sample_two

2
target/executable/parallel_map/.config.vsh.yaml
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@@ -231,7 +231,7 @@ build_info:
output: "target/executable/parallel_map"
executable: "target/executable/parallel_map/parallel_map"
viash_version: "0.9.0-RC6"
git_commit: "d18fe81ef5296d1c4d041865610f13e8992266e9"
git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

4
target/executable/parallel_map/parallel_map
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@@ -515,9 +515,9 @@ RUN wget -O $STAR_TARGET $STAR_SOURCE && \
rm $STAR_TARGET && rm -rf /tmp/STAR_$STAR_VERSION
LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
LABEL org.opencontainers.image.created="2024-08-20T15:14:30Z"
LABEL org.opencontainers.image.created="2024-08-20T15:27:42Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
LABEL org.opencontainers.image.revision="d18fe81ef5296d1c4d041865610f13e8992266e9"
LABEL org.opencontainers.image.revision="bdd7091d5b5982b84103a43fece50c608810e0aa"
LABEL org.opencontainers.image.version="main_pipeline"
VIASHDOCKER

2
target/nextflow/parallel_map/.config.vsh.yaml
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@@ -231,7 +231,7 @@ build_info:
output: "target/nextflow/parallel_map"
executable: "target/nextflow/parallel_map/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d18fe81ef5296d1c4d041865610f13e8992266e9"
git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/parallel_map/main.nf
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@@ -3059,7 +3059,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/parallel_map",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d18fe81ef5296d1c4d041865610f13e8992266e9",
"git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

206
target/nextflow/parallel_map/nextflow_schema.json Normal file
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@@ -0,0 +1,206 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "parallel_map",
"description": "Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n",
"type": "object",
"definitions": {
"input arguments" : {
"title": "Input arguments",
"type": "object",
"description": "No description",
"properties": {
"input_r1": {
"type":
"string",
"description": "Type: List of `file`, required, multiple_sep: `\":\"`. ",
"help_text": "Type: List of `file`, required, multiple_sep: `\":\"`. "
}
,
"input_r2": {
"type":
"string",
"description": "Type: List of `file`, required, multiple_sep: `\":\"`. ",
"help_text": "Type: List of `file`, required, multiple_sep: `\":\"`. "
}
,
"genomeDir": {
"type":
"string",
"description": "Type: `file`, required. STAR reference directory",
"help_text": "Type: `file`, required. STAR reference directory"
}
,
"barcodes": {
"type":
"string",
"description": "Type: List of `string`, required, multiple_sep: `\":\"`. The barcodes/wells to process",
"help_text": "Type: List of `string`, required, multiple_sep: `\":\"`. The barcodes/wells to process"
}
}
},
"barcode arguments" : {
"title": "Barcode arguments",
"type": "object",
"description": "No description",
"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",
"description": "Type: `integer`, required. The length of the UMIs",
"help_text": "Type: `integer`, required. The length of the UMIs"
}
,
"limitBAMsortRAM": {
"type":
"string",
"description": "Type: `string`, default: `10000000000`. ",
"help_text": "Type: `string`, default: `10000000000`. "
,
"default": "10000000000"
}
}
},
"runtime arguments" : {
"title": "Runtime arguments",
"type": "object",
"description": "No description",
"properties": {
"runThreadN": {
"type":
"integer",
"description": "Type: `integer`, default: `1`. Number of threads to use for a single STAR execution",
"help_text": "Type: `integer`, default: `1`. Number of threads to use for a single STAR execution."
,
"default": "1"
}
}
},
"output arguments" : {
"title": "Output arguments",
"type": "object",
"description": "No description",
"properties": {
"output": {
"type":
"string",
"description": "Type: List of `file`, required, default: `$id.$key.output_*./*`, multiple_sep: `\":\"`. Location of the output folders, 1 folder per barcode",
"help_text": "Type: List of `file`, required, default: `$id.$key.output_*./*`, multiple_sep: `\":\"`. Location of the output folders, 1 folder per barcode. The value used\nfor this argument must contain a \u0027*\u0027, which will be replaced with the\nbarcode to form the final output location for that barcode.\n"
,
"default": "$id.$key.output_*./*"
}
,
"joblog": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.joblog.txt`. Where to store the log file listing all the jobs",
"help_text": "Type: `file`, default: `$id.$key.joblog.txt`. Where to store the log file listing all the jobs."
,
"default": "$id.$key.joblog.txt"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input arguments"
},
{
"$ref": "#/definitions/barcode arguments"
},
{
"$ref": "#/definitions/runtime arguments"
},
{
"$ref": "#/definitions/output arguments"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

2
target/nextflow/workflows/htrnaseq/.config.vsh.yaml
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@@ -190,7 +190,7 @@ build_info:
output: "target/nextflow/workflows/htrnaseq"
executable: "target/nextflow/workflows/htrnaseq/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d18fe81ef5296d1c4d041865610f13e8992266e9"
git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/nextflow/workflows/well_demultiplex"

2
target/nextflow/workflows/htrnaseq/main.nf
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@@ -3030,7 +3030,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/htrnaseq",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d18fe81ef5296d1c4d041865610f13e8992266e9",
"git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/utils/groupLanes/.config.vsh.yaml
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@@ -136,7 +136,7 @@ build_info:
output: "target/nextflow/workflows/utils/groupLanes"
executable: "target/nextflow/workflows/utils/groupLanes/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d18fe81ef5296d1c4d041865610f13e8992266e9"
git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/workflows/utils/groupLanes/main.nf
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@@ -2943,7 +2943,7 @@ meta = [
"engine" : "native",
"output" : "target/nextflow/workflows/utils/groupLanes",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d18fe81ef5296d1c4d041865610f13e8992266e9",
"git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/utils/groupPairs/.config.vsh.yaml
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@@ -124,7 +124,7 @@ build_info:
output: "target/nextflow/workflows/utils/groupPairs"
executable: "target/nextflow/workflows/utils/groupPairs/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d18fe81ef5296d1c4d041865610f13e8992266e9"
git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/workflows/utils/groupPairs/main.nf
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@@ -2929,7 +2929,7 @@ meta = [
"engine" : "native",
"output" : "target/nextflow/workflows/utils/groupPairs",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d18fe81ef5296d1c4d041865610f13e8992266e9",
"git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/utils/groupWells/.config.vsh.yaml
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@@ -156,7 +156,7 @@ build_info:
output: "target/nextflow/workflows/utils/groupWells"
executable: "target/nextflow/workflows/utils/groupWells/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d18fe81ef5296d1c4d041865610f13e8992266e9"
git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/workflows/utils/groupWells/main.nf
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@@ -2967,7 +2967,7 @@ meta = [
"engine" : "native",
"output" : "target/nextflow/workflows/utils/groupWells",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d18fe81ef5296d1c4d041865610f13e8992266e9",
"git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/utils/splitWells/.config.vsh.yaml
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@@ -142,7 +142,7 @@ build_info:
output: "target/nextflow/workflows/utils/splitWells"
executable: "target/nextflow/workflows/utils/splitWells/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d18fe81ef5296d1c4d041865610f13e8992266e9"
git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
git_remote: "https://github.com/viash-hub/htrnaseq"
package_config:
name: "htrnaseq"

2
target/nextflow/workflows/utils/splitWells/main.nf
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@@ -2950,7 +2950,7 @@ meta = [
"engine" : "native",
"output" : "target/nextflow/workflows/utils/splitWells",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d18fe81ef5296d1c4d041865610f13e8992266e9",
"git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {

2
target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
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@@ -151,7 +151,7 @@ build_info:
output: "target/nextflow/workflows/well_demultiplex"
executable: "target/nextflow/workflows/well_demultiplex/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d18fe81ef5296d1c4d041865610f13e8992266e9"
git_commit: "bdd7091d5b5982b84103a43fece50c608810e0aa"
git_remote: "https://github.com/viash-hub/htrnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/cutadapt"

2
target/nextflow/workflows/well_demultiplex/main.nf
View File

@@ -2969,7 +2969,7 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/workflows/well_demultiplex",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d18fe81ef5296d1c4d041865610f13e8992266e9",
"git_commit" : "bdd7091d5b5982b84103a43fece50c608810e0aa",
"git_remote" : "https://github.com/viash-hub/htrnaseq"
},
"package_config" : {