diff --git a/CHANGELOG.md b/CHANGELOG.md index 9aa01b6..3bb38b9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# demultiplex v0.3.2 + +# Bug fixes + +* Ignore empty CSV entries when parsing sample information (PR #29). + # demultiplex v0.3.1 # Minor updates diff --git a/src/dataflow/gather_fastqs_and_validate/main.nf b/src/dataflow/gather_fastqs_and_validate/main.nf index ce8b90f..76c5d60 100644 --- a/src/dataflow/gather_fastqs_and_validate/main.nf +++ b/src/dataflow/gather_fastqs_and_validate/main.nf @@ -50,7 +50,10 @@ workflow run_wf { println "Found sample names column '${csv_items[sample_id_column_index]}'." return } - samples += csv_items[sample_id_column_index] + def candidate_sample_id = csv_items[sample_id_column_index] + if (candidate_sample_id?.trim()) { // Don't add empty csv entries. + samples += csv_items[sample_id_column_index] + } } // This return is important! (If 'true' is returned, the parsing stops.) return diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml index f71767b..3cf0ef8 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -141,9 +141,9 @@ 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: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv index 739e856..593ec31 100755 --- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv +++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv @@ -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="2024-12-11T15:28:43Z" +LABEL org.opencontainers.image.created="2024-12-11T17:49:17Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc" +LABEL org.opencontainers.image.revision="45accaa50e52c6b29c78259995293789f345c80d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index e5041e8..f6bd2bb 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -170,9 +170,9 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.0" - git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index 76bfba9..d7c1e80 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -482,9 +482,9 @@ 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="2024-12-11T15:28:44Z" +LABEL org.opencontainers.image.created="2024-12-11T17:49:17Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc" +LABEL org.opencontainers.image.revision="45accaa50e52c6b29c78259995293789f345c80d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index 3d9c84d..2450990 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -148,9 +148,9 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.0" - git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" package_config: name: "demultiplex" version: "main" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 600b94c..7ce066a 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -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="2024-12-11T15:28:44Z" +LABEL org.opencontainers.image.created="2024-12-11T17:49:18Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="5c096fce4015435019d81e2cc524a478f4034adc" +LABEL org.opencontainers.image.revision="45accaa50e52c6b29c78259995293789f345c80d" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index f04f040..eb0c36e 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -139,9 +139,9 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.0" - git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index 4f833f9..ce9a06e 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -2972,9 +2972,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.0", - "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-10-g5c096fc" + "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-11-g45accaa" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml index c553c7a..af62099 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -133,9 +133,9 @@ 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: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index 33006d5..2e8061c 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -2965,9 +2965,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.0", - "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-10-g5c096fc" + "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-11-g45accaa" }, "package_config" : { "name" : "demultiplex", @@ -3063,7 +3063,10 @@ workflow run_wf { println "Found sample names column '${csv_items[sample_id_column_index]}'." return } - samples += csv_items[sample_id_column_index] + def candidate_sample_id = csv_items[sample_id_column_index] + if (candidate_sample_id?.trim()) { // Don't add empty csv entries. + samples += csv_items[sample_id_column_index] + } } // This return is important! (If 'true' is returned, the parsing stops.) return diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index fa692fe..0ba0efe 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -220,9 +220,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" dependencies: - "target/nextflow/io/untar" - "target/nextflow/dataflow/gather_fastqs_and_validate" diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index 9f2c6d5..ddce380 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -3088,9 +3088,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.0", - "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-10-g5c096fc" + "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-11-g45accaa" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml index 7666617..a481238 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -141,9 +141,9 @@ 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: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index d667e1b..10d8522 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -2977,9 +2977,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.0", - "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-10-g5c096fc" + "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-11-g45accaa" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index 41711d9..823a726 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -170,9 +170,9 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.0" - git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index 3fba507..a27615b 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -3012,9 +3012,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.0", - "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-10-g5c096fc" + "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-11-g45accaa" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 0698743..4e1673d 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -148,9 +148,9 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.0" - git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" package_config: name: "demultiplex" version: "main" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index 4338c16..d5bed0f 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -2989,9 +2989,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.0", - "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-10-g5c096fc" + "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-11-g45accaa" }, "package_config" : { "name" : "demultiplex", diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index 12124e1..bc9fa22 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -182,9 +182,9 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.0" - git_commit: "5c096fce4015435019d81e2cc524a478f4034adc" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-10-g5c096fc" + git_commit: "45accaa50e52c6b29c78259995293789f345c80d" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.1.1-11-g45accaa" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index 478b058..1841758 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -3027,9 +3027,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.0", - "git_commit" : "5c096fce4015435019d81e2cc524a478f4034adc", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-10-g5c096fc" + "git_commit" : "45accaa50e52c6b29c78259995293789f345c80d", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.1.1-11-g45accaa" }, "package_config" : { "name" : "demultiplex",