vsh/demultiplex
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch main with version main (cfefb99)

Browse Source 
Build pipeline: viash-hub.demultiplex.main-ks8mz

Source commit: cfefb99ef0

Source message: Bump Viash version to 0.9.0
This commit is contained in:
CI
2024-09-12 12:30:59 +00:00
parent 54d722dcb7
commit 6c37efac8f
17 changed files with 393 additions and 192 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
View File

@@ -138,8 +138,8 @@ build_info:
engine: "native|native"
output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_remote: "https://github.com/viash-hub/demultiplex"
package_config:
name: "demultiplex"
@@ -149,7 +149,7 @@ package_config:
test_resources:
- path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
dest: "test_resources"
viash_version: "0.9.0-RC6"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

62
target/nextflow/dataflow/combine_samples/main.nf
View File

@@ -1,8 +1,8 @@
// combine_samples 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 ->
@@ -2945,8 +2971,8 @@ meta = [
"runner" : "nextflow",
"engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.0-RC6",
"git_commit" : "ed860bed30c98b981270f104cffbdb9b7f1ce141",
"viash_version" : "0.9.0",
"git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
"git_remote" : "https://github.com/viash-hub/demultiplex"
},
"package_config" : {
@@ -2961,7 +2987,7 @@ meta = [
}
]
},
"viash_version" : "0.9.0-RC6",
"viash_version" : "0.9.0",
"source" : "src",
"target" : "target",
"config_mods" : [

8
target/nextflow/dataflow/combine_samples/nextflow_schema.json
View File

@@ -57,8 +57,8 @@
"output_forward": {
"type":
"string",
"description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. ",
"help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. "
"description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\";\"`. "
,
"default": "$id.$key.output_forward_*.output_forward_*"
}
@@ -68,8 +68,8 @@
"output_reverse": {
"type":
"string",
"description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. ",
"help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. "
"description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. ",
"help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\";\"`. "
,
"default": "$id.$key.output_reverse_*.output_reverse_*"
}

6
target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
View File

@@ -132,8 +132,8 @@ build_info:
engine: "native|native"
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
viash_version: "0.9.0"
git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
git_remote: "https://github.com/viash-hub/demultiplex"
package_config:
name: "demultiplex"
@@ -143,7 +143,7 @@ package_config:
test_resources:
- path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
dest: "test_resources"
viash_version: "0.9.0-RC6"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

62
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
View File

@@ -1,8 +1,8 @@
// gather_fastqs_and_validate 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 ->
@@ -2938,8 +2964,8 @@ meta = [
"runner" : "nextflow",
"engine" : "native|native",
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
"viash_version" : "0.9.0-RC6",
"git_commit" : "ed860bed30c98b981270f104cffbdb9b7f1ce141",
"viash_version" : "0.9.0",
"git_commit" : "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f",
"git_remote" : "https://github.com/viash-hub/demultiplex"
},
"package_config" : {
@@ -2954,7 +2980,7 @@ meta = [
}
]
},
"viash_version" : "0.9.0-RC6",
"viash_version" : "0.9.0",
"source" : "src",
"target" : "target",
"config_mods" : [