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Build branch main with version main (0c27ec1)

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

Source commit: 0c27ec1436

Source message: Assert that demultiplexed FASTQ files are not empty (#40)
This commit is contained in:
CI
2025-03-27 16:12:48 +00:00
parent 26f9bf6da2
commit 51fdf9e8bf
22 changed files with 98 additions and 40 deletions
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6
CHANGELOG.md
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@@ -1,3 +1,9 @@
# demultiplex v0.3.8
## Bug fixes
* Provide a proper error when a FASTQ file is empty after demultiplexing (PR #40).
# demultiplex v0.3.7
## Minor updates

26
src/dataflow/gather_fastqs_and_validate/main.nf
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@@ -1,3 +1,26 @@
import java.util.zip.GZIPInputStream
import java.nio.file.Files
import java.io.BufferedInputStream
def is_empty(file_to_check){
/*
Checks if a file has content
*/
if (file_to_check.size() == 0) {
return true
}
def input_stream = Files.newInputStream(file_to_check)
def gzInputStream
try {
gzInputStream = new GZIPInputStream(new BufferedInputStream(input_stream))
} catch (java.io.EOFException ex) {
// This is not a gzipfile...
return false
}
def read_one_byte = gzInputStream.read()
return read_one_byte == -1
}
workflow run_wf {
take:
input_ch
@@ -78,6 +101,9 @@ workflow run_wf {
"Found forward: ${forward_fastq} and reverse: ${reverse_fastq}."
println "Found ${forward_fastq.size()} forward and ${reverse_fastq.size()} reverse " +
"fastq files for sample ${sample_id}"
assert forward_fastq.every{!is_empty(it)} && reverse_fastq.every{!is_empty(it)}:
"A fastq file for sample '${sample_id}' appears to be empty!"
def fastqs_state = [
"fastq_forward": forward_fastq,
"fastq_reverse": reverse_fastq,

4
target/executable/io/interop_summary_to_csv/.config.vsh.yaml
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@@ -146,9 +146,9 @@ build_info:
output: "target/executable/io/interop_summary_to_csv"
executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
package_config:
name: "demultiplex"
version: "main"

4
target/executable/io/interop_summary_to_csv/interop_summary_to_csv
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@@ -470,9 +470,9 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
LABEL org.opencontainers.image.created="2025-03-20T20:31:40Z"
LABEL org.opencontainers.image.created="2025-03-27T15:56:06Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="0acfda628d38430a7cdc21acf52878703b3b4bfc"
LABEL org.opencontainers.image.revision="0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/io/publish/.config.vsh.yaml
View File

@@ -196,9 +196,9 @@ build_info:
output: "target/executable/io/publish"
executable: "target/executable/io/publish/publish"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
package_config:
name: "demultiplex"
version: "main"

4
target/executable/io/publish/publish
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@@ -490,9 +490,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io publish"
LABEL org.opencontainers.image.created="2025-03-20T20:31:40Z"
LABEL org.opencontainers.image.created="2025-03-27T15:56:05Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="0acfda628d38430a7cdc21acf52878703b3b4bfc"
LABEL org.opencontainers.image.revision="0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/executable/io/untar/.config.vsh.yaml
View File

@@ -153,9 +153,9 @@ build_info:
output: "target/executable/io/untar"
executable: "target/executable/io/untar/untar"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
package_config:
name: "demultiplex"
version: "main"

4
target/executable/io/untar/untar
View File

@@ -476,9 +476,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component io untar"
LABEL org.opencontainers.image.created="2025-03-20T20:31:40Z"
LABEL org.opencontainers.image.created="2025-03-27T15:56:05Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
LABEL org.opencontainers.image.revision="0acfda628d38430a7cdc21acf52878703b3b4bfc"
LABEL org.opencontainers.image.revision="0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

4
target/nextflow/dataflow/combine_samples/.config.vsh.yaml
View File

@@ -162,9 +162,9 @@ build_info:
output: "target/nextflow/dataflow/combine_samples"
executable: "target/nextflow/dataflow/combine_samples/main.nf"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
package_config:
name: "demultiplex"
version: "main"

4
target/nextflow/dataflow/combine_samples/main.nf
View File

@@ -3000,9 +3000,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/combine_samples",
"viash_version" : "0.9.0",
"git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
"git_commit" : "0c27ec143671b3d9c985f2b5dc92f2a2065349d4",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-20-g0acfda6"
"git_tag" : "v0.1.1-21-g0c27ec1"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml
View File

@@ -138,9 +138,9 @@ build_info:
output: "target/nextflow/dataflow/gather_fastqs_and_validate"
executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
package_config:
name: "demultiplex"
version: "main"

30
target/nextflow/dataflow/gather_fastqs_and_validate/main.nf
View File

@@ -2973,9 +2973,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/dataflow/gather_fastqs_and_validate",
"viash_version" : "0.9.0",
"git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
"git_commit" : "0c27ec143671b3d9c985f2b5dc92f2a2065349d4",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-20-g0acfda6"
"git_tag" : "v0.1.1-21-g0c27ec1"
},
"package_config" : {
"name" : "demultiplex",
@@ -3019,6 +3019,29 @@ meta = [
// inner workflow
// user-provided Nextflow code
import java.util.zip.GZIPInputStream
import java.nio.file.Files
import java.io.BufferedInputStream
def is_empty(file_to_check){
/*
Checks if a file has content
*/
if (file_to_check.size() == 0) {
return true
}
def input_stream = Files.newInputStream(file_to_check)
def gzInputStream
try {
gzInputStream = new GZIPInputStream(new BufferedInputStream(input_stream))
} catch (java.io.EOFException ex) {
// This is not a gzipfile...
return false
}
def read_one_byte = gzInputStream.read()
return read_one_byte == -1
}
workflow run_wf {
take:
input_ch
@@ -3099,6 +3122,9 @@ workflow run_wf {
"Found forward: ${forward_fastq} and reverse: ${reverse_fastq}."
println "Found ${forward_fastq.size()} forward and ${reverse_fastq.size()} reverse " +
"fastq files for sample ${sample_id}"
assert forward_fastq.every{!is_empty(it)} && reverse_fastq.every{!is_empty(it)}:
"A fastq file for sample '${sample_id}' appears to be empty!"
def fastqs_state = [
"fastq_forward": forward_fastq,
"fastq_reverse": reverse_fastq,

4
target/nextflow/demultiplex/.config.vsh.yaml
View File

@@ -244,9 +244,9 @@ build_info:
output: "target/nextflow/demultiplex"
executable: "target/nextflow/demultiplex/main.nf"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
dependencies:
- "target/nextflow/io/untar"
- "target/nextflow/dataflow/gather_fastqs_and_validate"

4
target/nextflow/demultiplex/main.nf
View File

@@ -3120,9 +3120,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/demultiplex",
"viash_version" : "0.9.0",
"git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
"git_commit" : "0c27ec143671b3d9c985f2b5dc92f2a2065349d4",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-20-g0acfda6"
"git_tag" : "v0.1.1-21-g0c27ec1"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml
View File

@@ -146,9 +146,9 @@ build_info:
output: "target/nextflow/io/interop_summary_to_csv"
executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
package_config:
name: "demultiplex"
version: "main"

4
target/nextflow/io/interop_summary_to_csv/main.nf
View File

@@ -2985,9 +2985,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/interop_summary_to_csv",
"viash_version" : "0.9.0",
"git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
"git_commit" : "0c27ec143671b3d9c985f2b5dc92f2a2065349d4",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-20-g0acfda6"
"git_tag" : "v0.1.1-21-g0c27ec1"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/io/publish/.config.vsh.yaml
View File

@@ -196,9 +196,9 @@ build_info:
output: "target/nextflow/io/publish"
executable: "target/nextflow/io/publish/main.nf"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
package_config:
name: "demultiplex"
version: "main"

4
target/nextflow/io/publish/main.nf
View File

@@ -3044,9 +3044,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/publish",
"viash_version" : "0.9.0",
"git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
"git_commit" : "0c27ec143671b3d9c985f2b5dc92f2a2065349d4",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-20-g0acfda6"
"git_tag" : "v0.1.1-21-g0c27ec1"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/io/untar/.config.vsh.yaml
View File

@@ -153,9 +153,9 @@ build_info:
output: "target/nextflow/io/untar"
executable: "target/nextflow/io/untar/main.nf"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
package_config:
name: "demultiplex"
version: "main"

4
target/nextflow/io/untar/main.nf
View File

@@ -2997,9 +2997,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/io/untar",
"viash_version" : "0.9.0",
"git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
"git_commit" : "0c27ec143671b3d9c985f2b5dc92f2a2065349d4",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-20-g0acfda6"
"git_tag" : "v0.1.1-21-g0c27ec1"
},
"package_config" : {
"name" : "demultiplex",

4
target/nextflow/runner/.config.vsh.yaml
View File

@@ -192,9 +192,9 @@ build_info:
output: "target/nextflow/runner"
executable: "target/nextflow/runner/main.nf"
viash_version: "0.9.0"
git_commit: "0acfda628d38430a7cdc21acf52878703b3b4bfc"
git_commit: "0c27ec143671b3d9c985f2b5dc92f2a2065349d4"
git_remote: "https://github.com/viash-hub/demultiplex"
git_tag: "v0.1.1-20-g0acfda6"
git_tag: "v0.1.1-21-g0c27ec1"
dependencies:
- "target/nextflow/demultiplex"
- "target/nextflow/io/publish"

4
target/nextflow/runner/main.nf
View File

@@ -3040,9 +3040,9 @@ meta = [
"engine" : "native|native",
"output" : "target/nextflow/runner",
"viash_version" : "0.9.0",
"git_commit" : "0acfda628d38430a7cdc21acf52878703b3b4bfc",
"git_commit" : "0c27ec143671b3d9c985f2b5dc92f2a2065349d4",
"git_remote" : "https://github.com/viash-hub/demultiplex",
"git_tag" : "v0.1.1-20-g0acfda6"
"git_tag" : "v0.1.1-21-g0c27ec1"
},
"package_config" : {
"name" : "demultiplex",