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Build branch main with version main (0c8a7eb)

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Build pipeline: viash-hub.rnaseq.main-nn8dl

Source commit: 0c8a7eb648

Source message: remove citation
This commit is contained in:
CI
2024-11-27 11:54:48 +00:00
parent 14e0d12189
commit 93ac6aad2e
325 changed files with 30328 additions and 46408 deletions
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20
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
View File

@@ -116,7 +116,7 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
- type: "double"
name: "--kallisto_quant_fragment_length"
description: "For single-end mode only, the estimated average fragment length\
\ to use for quantification with Kallisto."
@@ -125,7 +125,7 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
- type: "double"
name: "--kallisto_quant_fragment_length_sd"
description: "For single-end mode only, the estimated standard deviation of the\
\ fragment length for quantification with Kallisto."
@@ -194,15 +194,17 @@ dependencies:
- name: "salmon/salmon_quant"
repository:
type: "vsh"
repo: "vsh/biobox"
repo: "biobox"
tag: "main"
- name: "kallisto/kallisto_quant"
repository:
type: "local"
type: "vsh"
repo: "biobox"
tag: "main"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
repo: "biobox"
tag: "main"
- type: "vsh"
name: "craftbox"
@@ -283,11 +285,11 @@ build_info:
output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant"
package_config:
name: "rnaseq"
version: "main"
@@ -298,7 +300,7 @@ package_config:
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
repo: "biobox"
tag: "main"
- type: "vsh"
name: "craftbox"

54
target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant
View File

@@ -227,12 +227,12 @@ function ViashHelp {
echo " object"
echo ""
echo " --kallisto_quant_fragment_length"
echo " type: integer"
echo " type: double"
echo " For single-end mode only, the estimated average fragment length to use"
echo " for quantification with Kallisto."
echo ""
echo " --kallisto_quant_fragment_length_sd"
echo " type: integer"
echo " type: double"
echo " For single-end mode only, the estimated standard deviation of the"
echo " fragment length for quantification with Kallisto."
echo ""
@@ -645,14 +645,14 @@ fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ]]; then
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--kallisto_quant_fragment_length' has to be an integer. Use "--help" to get more information on the parameters.
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
ViashError '--kallisto_quant_fragment_length' has to be a double. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ]]; then
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--kallisto_quant_fragment_length_sd' has to be an integer. Use "--help" to get more information on the parameters.
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
ViashError '--kallisto_quant_fragment_length_sd' has to be a double. Use "--help" to get more information on the parameters.
exit 1
fi
fi
@@ -779,8 +779,8 @@ fi
# set dependency paths
VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_quant/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
@@ -859,22 +859,32 @@ workflow run_wf {
[ id, mod_state ]
}
| kallisto_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
fromState: [
"input": "input",
"paired": "paired",
"gtf": "gtf",
"index": "kallisto_index",
"fragment_length": "kallisto_quant_fragment_length",
"fragment_length_sd": "kallisto_quant_fragment_length_sd"
],
toState: [
"quant_out_dir": "output",
"kallisto_quant_results_file": "quant_results_file",
"pseudo_multiqc": "log"
| kallisto_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
fromState: { id, state ->
def fr_stranded = state.strandedness == 'forward'
def rf_stranded = state.strandedness == 'reverse'
[
input: state.input,
index: state.kallisto_index,
fragment_length: state.kallisto_quant_fragment_length,
sd: state.kallisto_quant_fragment_length_sd,
single: !state.paired,
fr_stranded: fr_stranded,
rf_stranded: rf_stranded,
]
)
},
args: [log: "kallisto_quant.log"],
toState: { id, output_state, state ->
def neKeys = [
"quant_out_dir": output_state["output_dir"],
"kallisto_quant_results_file": output_state["output_dir"] + "/abundance.tsv",
"pseudo_multiqc": output_state["log"]
]
def new_state = state + newKeys
return new_state
}
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }