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Build branch main with version main (32dc807)

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Build pipeline: viash-hub.playground.main-n876l

Source commit: 32dc80723a

Source message: Emtpy commit
This commit is contained in:
CI
2025-02-26 15:29:31 +00:00
parent fbf20cbd8a
commit c0bd36f2eb
5 changed files with 73 additions and 46 deletions
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2
_viash.yaml
View File

@@ -7,7 +7,7 @@ links:
issue_tracker: https://github.com/viash-hub/playground/issues
repository: https://github.com/viash-hub/playground
viash_version: 0.9.0-RC6
viash_version: 0.9.0
config_mods: |
.requirements.commands := ['ps']

3
src/mapping_and_qc/config.vsh.yaml
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@@ -1,5 +1,6 @@
name: mapping_and_qc
description: Run STAR and QC
argument_groups:
- name: Input arguments
arguments:
@@ -27,7 +28,6 @@ resources:
path: main.nf
entrypoint: run_wf
dependencies:
- name: cutadapt
repository: bb
@@ -45,6 +45,7 @@ repositories:
type: vsh
repo: vsh/biobox
tag: main
runners:
- type: nextflow

6
target/nextflow/mapping_and_qc/.config.vsh.yaml
View File

@@ -161,8 +161,8 @@ build_info:
engine: "native|native"
output: "target/nextflow/mapping_and_qc"
executable: "target/nextflow/mapping_and_qc/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "d87d344d4e46dc6f938e57a009607946ed31447c"
viash_version: "0.9.0"
git_commit: "32dc80723acb5d5861c7acd7c6c07ef4cd1a6ee7"
git_remote: "https://github.com/viash-hub/playground"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/cutadapt"
@@ -176,7 +176,7 @@ package_config:
description: "A collection of bioinformatics pipelines to illustrate the use of\
\ biobox (and biotools).\n"
info: null
viash_version: "0.9.0-RC6"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

62
target/nextflow/mapping_and_qc/main.nf
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@@ -1,8 +1,8 @@
// mapping_and_qc main
//
// This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
// derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
// Data Intuitive.
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
// Intuitive.
//
// The component may contain files which fall under a different license. The
// authors of this component should specify the license in the header of such
@@ -760,8 +760,11 @@ def runEach(Map args) {
def fromState_ = args.fromState
def toState_ = args.toState
def filter_ = args.filter
def runIf_ = args.runIf
def id_ = args.id
assert !runIf_ || runIf_ instanceof Closure: "runEach: must pass a Closure to runIf."
workflow runEachWf {
take: input_ch
main:
@@ -783,7 +786,20 @@ def runEach(Map args) {
[new_id] + tup.drop(1)
}
: filter_ch
def data_ch = id_ch | map{tup ->
def chPassthrough = null
def chRun = null
if (runIf_) {
def idRunIfBranch = id_ch.branch{ tup ->
run: runIf_(tup[0], tup[1], comp_)
passthrough: true
}
chPassthrough = idRunIfBranch.passthrough
chRun = idRunIfBranch.run
} else {
chRun = id_ch
chPassthrough = Channel.empty()
}
def data_ch = chRun | map{tup ->
def new_data = tup[1]
if (fromState_ instanceof Map) {
new_data = fromState_.collectEntries{ key0, key1 ->
@@ -821,8 +837,11 @@ def runEach(Map args) {
[tup[0], new_state] + tup.drop(3)
}
: out_ch
def return_ch = post_ch
| concat(chPassthrough)
post_ch
return_ch
}
// mix all results
@@ -1598,8 +1617,8 @@ def findStates(Map params, Map config) {
// construct renameMap
if (args.rename_keys) {
def renameMap = args.rename_keys.collectEntries{renameString ->
def split = renameString.split(";")
assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
def split = renameString.split(":")
assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey', or 'newKey:oldKey;newKey:oldKey' in case of multiple values"
split
}
@@ -1709,7 +1728,9 @@ def publishStates(Map args) {
def yamlFilename = yamlTemplate_
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
// TODO: do the pathnames in state_ match up with the outputFilenames_?
@@ -1780,7 +1801,9 @@ def publishStatesByConfig(Map args) {
def yamlTemplate = params.containsKey("output_state") ? params.output_state : '$id.$key.state.yaml'
def yamlFilename = yamlTemplate
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
def yamlDir = java.nio.file.Paths.get(yamlFilename).getParent()
// the processed state is a list of [key, value, inputPath, outputFilename] tuples, where
@@ -1822,7 +1845,9 @@ def publishStatesByConfig(Map args) {
// instantiate the template
def filename = filenameTemplate
.replaceAll('\\$id', id_)
.replaceAll('\\$\\{id\\}', id_)
.replaceAll('\\$key', key_)
.replaceAll('\\$\\{key\\}', key_)
if (par.multiple) {
// if the parameter is multiple: true, the filename
// should contain a wildcard '*' that is replaced with
@@ -2626,30 +2651,31 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
tuple
}
def chModifiedFiltered = workflowArgs.filter ?
chModified | filter{workflowArgs.filter(it)} :
chModified
def chRun = null
def chPassthrough = null
if (workflowArgs.runIf) {
def runIfBranch = chModifiedFiltered.branch{ tup ->
def runIfBranch = chModified.branch{ tup ->
run: workflowArgs.runIf(tup[0], tup[1])
passthrough: true
}
chRun = runIfBranch.run
chPassthrough = runIfBranch.passthrough
} else {
chRun = chModifiedFiltered
chRun = chModified
chPassthrough = Channel.empty()
}
def chRunFiltered = workflowArgs.filter ?
chRun | filter{workflowArgs.filter(it)} :
chRun
def chArgs = workflowArgs.fromState ?
chRun | map{
chRunFiltered | map{
def new_data = workflowArgs.fromState(it.take(2))
[it[0], new_data]
} :
chRun | map {tup -> tup.take(2)}
chRunFiltered | map {tup -> tup.take(2)}
// fill in defaults
def chArgsWithDefaults = chArgs
@@ -2720,7 +2746,7 @@ def workflowFactory(Map args, Map defaultWfArgs, Map meta) {
// | view{"chInitialOutput: ${it.take(3)}"}
// join the output [prev_id, new_id, output] with the previous state [prev_id, state, ...]
def chNewState = safeJoin(chInitialOutput, chModifiedFiltered, key_)
def chNewState = safeJoin(chInitialOutput, chRunFiltered, key_)
// input tuple format: [join_id, id, output, prev_state, ...]
// output tuple format: [join_id, id, new_state, ...]
| map{ tup ->
@@ -2988,15 +3014,15 @@ meta = [
"runner" : "nextflow",
"engine" : "native|native",
"output" : "target/nextflow/mapping_and_qc",
"viash_version" : "0.9.0-RC6",
"git_commit" : "d87d344d4e46dc6f938e57a009607946ed31447c",
"viash_version" : "0.9.0",
"git_commit" : "32dc80723acb5d5861c7acd7c6c07ef4cd1a6ee7",
"git_remote" : "https://github.com/viash-hub/playground"
},
"package_config" : {
"name" : "playground",
"version" : "main",
"description" : "A collection of bioinformatics pipelines to illustrate the use of biobox (and biotools).\n",
"viash_version" : "0.9.0-RC6",
"viash_version" : "0.9.0",
"source" : "src",
"target" : "target",
"config_mods" : [

46
test_data.sh
View File

@@ -12,56 +12,56 @@ if [ ! -f "$TEST_DATA_DIR/SRR1569895_1.fastq" ] || [ ! -f "$TEST_DATA_DIR/SRR156
docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1569895
fi
if [ ! -f "$TEST_DATA_DIR/SRR1570800_1.fastq" ] || [ ! -f "$TEST_DATA_DIR/SRR1570800_2.fastq" ]; then
docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1570800
docker run -t --rm -v $PWD:/output:rw -w /output/test_data ncbi/sra-tools fasterq-dump -e 2 -p SRR1570800
fi
head -n 10000 "$TEST_DATA_DIR/SRR1569895_1.fastq" > "$TEST_DATA_DIR/SRR1569895_1_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1569895_2.fastq" > "$TEST_DATA_DIR/SRR1569895_2_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1570800_1.fastq" > "$TEST_DATA_DIR/SRR1570800_1_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1570800_2.fastq" > "$TEST_DATA_DIR/SRR1570800_2_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1569895_1.fastq" >"$TEST_DATA_DIR/SRR1569895_1_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1569895_2.fastq" >"$TEST_DATA_DIR/SRR1569895_2_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1570800_1.fastq" >"$TEST_DATA_DIR/SRR1570800_1_subsample.fastq"
head -n 10000 "$TEST_DATA_DIR/SRR1570800_2.fastq" >"$TEST_DATA_DIR/SRR1570800_2_subsample.fastq"
export NXF_SCM_FILE="$TEST_DATA_DIR/scm.config"
cat > $NXF_SCM_FILE << EOF
cat >$NXF_SCM_FILE <<EOF
providers {
vsh {
platform = 'gitlab'
server = 'https://viash-hub.com/'
server = 'https://packages.viash-hub.com/'
}
}
EOF
if [ ! -f "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz" ]; then
wget http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_Current_Release.tgz \
-O "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz"
-O "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz"
fi
if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release" ]; then
nextflow run vsh/craftbox -hub vsh -r main -main-script target/nextflow/untar/main.nf \
-profile docker \
--input "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz" \
--output "S288C_reference_genome_Current_Release" \
--publish_dir "$TEST_DATA_DIR"
-profile docker \
--input "$TEST_DATA_DIR/S288C_reference_genome_Current_Release.tgz" \
--output "S288C_reference_genome_Current_Release" \
--publish_dir "$TEST_DATA_DIR"
fi
gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz" > "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff"
gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa.gz" >"$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
gunzip -c "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz" >"$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff"
sed -i -e 's/^.*chromosome=\(.*\)\]$/>chr\1/' "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa"
if [ ! -d "$TEST_DATA_DIR/S288C_reference_genome_Current_Release_STAR" ]; then
nextflow run vsh/biobox -hub vsh -r main -main-script target/nextflow/star/star_genome_generate/main.nf \
-profile docker \
--genome_fasta_files "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa" \
--sjdb_gtf_file "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff" \
--sjdb_gtf_tag_exon_parent_transcript Parent \
--sjdb_overhang 100 \
--publish_dir "$TEST_DATA_DIR" \
--sjdb_gtf_feature_exon noncoding_exon \
--index S288C_reference_genome_Current_Release_STAR
-profile docker \
--genome_fasta_files "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/S288C_reference_sequence_R64-5-1_20240529.fsa" \
--sjdb_gtf_file "$TEST_DATA_DIR/S288C_reference_genome_Current_Release/saccharomyces_cerevisiae_R64-5-1_20240529.gff" \
--sjdb_gtf_tag_exon_parent_transcript Parent \
--sjdb_overhang 100 \
--publish_dir "$TEST_DATA_DIR" \
--sjdb_gtf_feature_exon noncoding_exon \
--index S288C_reference_genome_Current_Release_STAR
fi
PARAMS_FILE=params_file.yaml
cat > $PARAMS_FILE << EOF
cat >$PARAMS_FILE <<EOF
param_list:
- id: SRR1569895
input_r1: $TEST_DATA_DIR/SRR1569895_1_subsample.fastq