From e62fdec9e521721787eb7481e62e28ded71a3737 Mon Sep 17 00:00:00 2001 From: rcannood Date: Wed, 3 May 2023 21:07:10 +0000 Subject: [PATCH] Deploy for release 0.1.1 from f639468c9d0ed115776e10d0f7a3330fff04ab20 --- CHANGELOG.md | 4 ++-- src/mapping/process_smartseq2/auto.vsh.yaml | 9 ++++----- .../docker/demux/spaceranger_mkfastq/.config.vsh.yaml | 2 +- .../demux/spaceranger_mkfastq/spaceranger_mkfastq | 4 ++-- .../docker/mapping/spaceranger_count/.config.vsh.yaml | 2 +- .../docker/mapping/spaceranger_count/spaceranger_count | 4 ++-- .../multiomics/cellranger_arc_aggr/.config.vsh.yaml | 2 +- .../multiomics/cellranger_arc_aggr/cellranger_arc_aggr | 4 ++-- .../multiomics/cellranger_arc_count/.config.vsh.yaml | 2 +- .../cellranger_arc_count/cellranger_arc_count | 4 ++-- .../multiomics/cellranger_cite_seq/.config.vsh.yaml | 2 +- .../multiomics/cellranger_cite_seq/cellranger_cite_seq | 4 ++-- .../operations/create_runner_script/.config.vsh.yaml | 2 +- .../create_runner_script/create_runner_script | 4 ++-- .../native/demux/spaceranger_mkfastq/.config.vsh.yaml | 2 +- .../native/mapping/spaceranger_count/.config.vsh.yaml | 2 +- .../multiomics/cellranger_arc_aggr/.config.vsh.yaml | 2 +- .../multiomics/cellranger_arc_count/.config.vsh.yaml | 2 +- .../multiomics/cellranger_cite_seq/.config.vsh.yaml | 2 +- .../operations/create_runner_script/.config.vsh.yaml | 2 +- .../demux/spaceranger_mkfastq/.config.vsh.yaml | 2 +- target/nextflow/demux/spaceranger_mkfastq/main.nf | 2 +- target/nextflow/mapping/process_10x/.config.vsh.yaml | 2 +- target/nextflow/mapping/process_10x/main.nf | 2 +- .../nextflow/mapping/process_10x_auto/.config.vsh.yaml | 2 +- target/nextflow/mapping/process_10x_auto/main.nf | 2 +- .../mapping/process_smartseq2/.config.vsh.yaml | 2 +- target/nextflow/mapping/process_smartseq2/main.nf | 2 +- .../mapping/process_smartseq2_auto/.config.vsh.yaml | 10 +++++----- target/nextflow/mapping/process_smartseq2_auto/main.nf | 4 ++-- .../mapping/process_smartseq2_auto/nextflow.config | 2 +- .../process_smartseq2_auto/nextflow_schema.json | 2 +- .../mapping/spaceranger_count/.config.vsh.yaml | 2 +- target/nextflow/mapping/spaceranger_count/main.nf | 2 +- target/nextflow/tabula_sapiens/concat/.config.vsh.yaml | 2 +- target/nextflow/tabula_sapiens/concat/main.nf | 2 +- 36 files changed, 51 insertions(+), 52 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 27f56b2a..16853ed1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,8 @@ # utilities 0.1.1 -* `mapping/process_10x_auto`: Allow grouping input fastqs per folder or via a custom regex statement. +* `mapping/process_smartseq2_auto`: Allow grouping input fastqs per folder or via a custom regex statement. -* `mapping/process_10x_auto`: Add more documentation to the arguments to clarify regex usage. +* `mapping/process_smartseq2_auto`: Add more documentation to the arguments to clarify regex usage. # utilities 0.1.0 diff --git a/src/mapping/process_smartseq2/auto.vsh.yaml b/src/mapping/process_smartseq2/auto.vsh.yaml index 2423b2bc..3a91173d 100644 --- a/src/mapping/process_smartseq2/auto.vsh.yaml +++ b/src/mapping/process_smartseq2/auto.vsh.yaml @@ -11,11 +11,10 @@ functionality: * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`. * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`. * Write the list of samples as a yaml in the output directory. - * Map the reads using Cell Ranger - * Convert the Cell Ranger output to h5mu - * Remove ambient RNA with CellBender - * Remove cells with less than 100 genes or 1000 reads. - * Make the cell names unique + * Map the reads using Star + * Sort counts with samtools + * Convert to count table with HTSeq + * Compute QC metrics with MultiQC * Output one h5mu file per sample Concatenating the invididual h5mu files into one h5mu file is a separate pipeline. diff --git a/target/docker/demux/spaceranger_mkfastq/.config.vsh.yaml b/target/docker/demux/spaceranger_mkfastq/.config.vsh.yaml index 815b6ae8..80f87799 100644 --- a/target/docker/demux/spaceranger_mkfastq/.config.vsh.yaml +++ b/target/docker/demux/spaceranger_mkfastq/.config.vsh.yaml @@ -79,5 +79,5 @@ info: output: "/home/runner/work/utilities/utilities/target/docker/demux/spaceranger_mkfastq" executable: "/home/runner/work/utilities/utilities/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq b/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq index e85dda00..aa82d429 100755 --- a/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq +++ b/target/docker/demux/spaceranger_mkfastq/spaceranger_mkfastq @@ -399,9 +399,9 @@ FROM ghcr.io/data-intuitive/spaceranger:latest RUN : LABEL org.opencontainers.image.description="Companion container for running component demux spaceranger_mkfastq" -LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z" +LABEL org.opencontainers.image.created="2023-05-03T21:05:52Z" LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities" -LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b" +LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20" LABEL org.opencontainers.image.version="0.1.1" VIASHDOCKER } diff --git a/target/docker/mapping/spaceranger_count/.config.vsh.yaml b/target/docker/mapping/spaceranger_count/.config.vsh.yaml index 2c751eab..9672fc7a 100644 --- a/target/docker/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/docker/mapping/spaceranger_count/.config.vsh.yaml @@ -129,5 +129,5 @@ info: output: "/home/runner/work/utilities/utilities/target/docker/mapping/spaceranger_count" executable: "/home/runner/work/utilities/utilities/target/docker/mapping/spaceranger_count/spaceranger_count" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/docker/mapping/spaceranger_count/spaceranger_count b/target/docker/mapping/spaceranger_count/spaceranger_count index 974bdee4..86cc3a3f 100755 --- a/target/docker/mapping/spaceranger_count/spaceranger_count +++ b/target/docker/mapping/spaceranger_count/spaceranger_count @@ -423,9 +423,9 @@ FROM ghcr.io/data-intuitive/spaceranger:latest RUN : LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count" -LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z" +LABEL org.opencontainers.image.created="2023-05-03T21:05:53Z" LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities" -LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b" +LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20" LABEL org.opencontainers.image.version="0.1.1" VIASHDOCKER } diff --git a/target/docker/multiomics/cellranger_arc_aggr/.config.vsh.yaml b/target/docker/multiomics/cellranger_arc_aggr/.config.vsh.yaml index 118a0592..21f47406 100644 --- a/target/docker/multiomics/cellranger_arc_aggr/.config.vsh.yaml +++ b/target/docker/multiomics/cellranger_arc_aggr/.config.vsh.yaml @@ -105,5 +105,5 @@ info: output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_aggr" executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr b/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr index 2a25573b..b612c144 100755 --- a/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr +++ b/target/docker/multiomics/cellranger_arc_aggr/cellranger_arc_aggr @@ -418,9 +418,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "numpy" "pandas" "scanpy" LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_arc_aggr" -LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z" +LABEL org.opencontainers.image.created="2023-05-03T21:05:53Z" LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities" -LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b" +LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20" LABEL org.opencontainers.image.version="0.1.1" VIASHDOCKER } diff --git a/target/docker/multiomics/cellranger_arc_count/.config.vsh.yaml b/target/docker/multiomics/cellranger_arc_count/.config.vsh.yaml index 326b4255..1e03b373 100644 --- a/target/docker/multiomics/cellranger_arc_count/.config.vsh.yaml +++ b/target/docker/multiomics/cellranger_arc_count/.config.vsh.yaml @@ -97,5 +97,5 @@ info: output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_count" executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count b/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count index 3122e7ad..668e69fe 100755 --- a/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count +++ b/target/docker/multiomics/cellranger_arc_count/cellranger_arc_count @@ -416,9 +416,9 @@ FROM ghcr.io/data-intuitive/cellranger_arc:2.0 RUN : LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_arc_count" -LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z" +LABEL org.opencontainers.image.created="2023-05-03T21:05:53Z" LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities" -LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b" +LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20" LABEL org.opencontainers.image.version="0.1.1" VIASHDOCKER } diff --git a/target/docker/multiomics/cellranger_cite_seq/.config.vsh.yaml b/target/docker/multiomics/cellranger_cite_seq/.config.vsh.yaml index 253f5d3b..7e77302b 100644 --- a/target/docker/multiomics/cellranger_cite_seq/.config.vsh.yaml +++ b/target/docker/multiomics/cellranger_cite_seq/.config.vsh.yaml @@ -95,5 +95,5 @@ info: output: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_cite_seq" executable: "/home/runner/work/utilities/utilities/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq b/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq index 84e6762d..5a533792 100755 --- a/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq +++ b/target/docker/multiomics/cellranger_cite_seq/cellranger_cite_seq @@ -409,9 +409,9 @@ FROM ghcr.io/data-intuitive/cellranger_arc:2.0 RUN : LABEL org.opencontainers.image.description="Companion container for running component multiomics cellranger_cite_seq" -LABEL org.opencontainers.image.created="2023-05-03T20:09:53Z" +LABEL org.opencontainers.image.created="2023-05-03T21:05:54Z" LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities" -LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b" +LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20" LABEL org.opencontainers.image.version="0.1.1" VIASHDOCKER } diff --git a/target/docker/operations/create_runner_script/.config.vsh.yaml b/target/docker/operations/create_runner_script/.config.vsh.yaml index 3bcd8ded..76a39320 100644 --- a/target/docker/operations/create_runner_script/.config.vsh.yaml +++ b/target/docker/operations/create_runner_script/.config.vsh.yaml @@ -122,5 +122,5 @@ info: output: "/home/runner/work/utilities/utilities/target/docker/operations/create_runner_script" executable: "/home/runner/work/utilities/utilities/target/docker/operations/create_runner_script/create_runner_script" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/docker/operations/create_runner_script/create_runner_script b/target/docker/operations/create_runner_script/create_runner_script index 3f1d24e1..10cde374 100755 --- a/target/docker/operations/create_runner_script/create_runner_script +++ b/target/docker/operations/create_runner_script/create_runner_script @@ -426,9 +426,9 @@ FROM python:3.10 RUN : LABEL org.opencontainers.image.description="Companion container for running component operations create_runner_script" -LABEL org.opencontainers.image.created="2023-05-03T20:09:52Z" +LABEL org.opencontainers.image.created="2023-05-03T21:05:52Z" LABEL org.opencontainers.image.source="https://github.com/czbiohub/utilities" -LABEL org.opencontainers.image.revision="f4bc99bf82a915a68541bcfd58b146064c8dba2b" +LABEL org.opencontainers.image.revision="f639468c9d0ed115776e10d0f7a3330fff04ab20" LABEL org.opencontainers.image.version="0.1.1" VIASHDOCKER } diff --git a/target/native/demux/spaceranger_mkfastq/.config.vsh.yaml b/target/native/demux/spaceranger_mkfastq/.config.vsh.yaml index aecbc4ea..ef50324a 100644 --- a/target/native/demux/spaceranger_mkfastq/.config.vsh.yaml +++ b/target/native/demux/spaceranger_mkfastq/.config.vsh.yaml @@ -79,5 +79,5 @@ info: output: "/home/runner/work/utilities/utilities/target/native/demux/spaceranger_mkfastq" executable: "/home/runner/work/utilities/utilities/target/native/demux/spaceranger_mkfastq/spaceranger_mkfastq" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/native/mapping/spaceranger_count/.config.vsh.yaml b/target/native/mapping/spaceranger_count/.config.vsh.yaml index 7c327fa0..e54dc853 100644 --- a/target/native/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/native/mapping/spaceranger_count/.config.vsh.yaml @@ -129,5 +129,5 @@ info: output: "/home/runner/work/utilities/utilities/target/native/mapping/spaceranger_count" executable: "/home/runner/work/utilities/utilities/target/native/mapping/spaceranger_count/spaceranger_count" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/native/multiomics/cellranger_arc_aggr/.config.vsh.yaml b/target/native/multiomics/cellranger_arc_aggr/.config.vsh.yaml index c9f76440..a207bb2e 100644 --- a/target/native/multiomics/cellranger_arc_aggr/.config.vsh.yaml +++ b/target/native/multiomics/cellranger_arc_aggr/.config.vsh.yaml @@ -105,5 +105,5 @@ info: output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_aggr" executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_aggr/cellranger_arc_aggr" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/native/multiomics/cellranger_arc_count/.config.vsh.yaml b/target/native/multiomics/cellranger_arc_count/.config.vsh.yaml index 497570fc..390b9d26 100644 --- a/target/native/multiomics/cellranger_arc_count/.config.vsh.yaml +++ b/target/native/multiomics/cellranger_arc_count/.config.vsh.yaml @@ -97,5 +97,5 @@ info: output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_count" executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_arc_count/cellranger_arc_count" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/native/multiomics/cellranger_cite_seq/.config.vsh.yaml b/target/native/multiomics/cellranger_cite_seq/.config.vsh.yaml index 45690324..fb806aea 100644 --- a/target/native/multiomics/cellranger_cite_seq/.config.vsh.yaml +++ b/target/native/multiomics/cellranger_cite_seq/.config.vsh.yaml @@ -95,5 +95,5 @@ info: output: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_cite_seq" executable: "/home/runner/work/utilities/utilities/target/native/multiomics/cellranger_cite_seq/cellranger_cite_seq" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/native/operations/create_runner_script/.config.vsh.yaml b/target/native/operations/create_runner_script/.config.vsh.yaml index d21d8285..1c77f3c5 100644 --- a/target/native/operations/create_runner_script/.config.vsh.yaml +++ b/target/native/operations/create_runner_script/.config.vsh.yaml @@ -122,5 +122,5 @@ info: output: "/home/runner/work/utilities/utilities/target/native/operations/create_runner_script" executable: "/home/runner/work/utilities/utilities/target/native/operations/create_runner_script/create_runner_script" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/nextflow/demux/spaceranger_mkfastq/.config.vsh.yaml b/target/nextflow/demux/spaceranger_mkfastq/.config.vsh.yaml index a68f81cc..5a440d42 100644 --- a/target/nextflow/demux/spaceranger_mkfastq/.config.vsh.yaml +++ b/target/nextflow/demux/spaceranger_mkfastq/.config.vsh.yaml @@ -79,5 +79,5 @@ info: output: "/home/runner/work/utilities/utilities/target/nextflow/demux/spaceranger_mkfastq" executable: "/home/runner/work/utilities/utilities/target/nextflow/demux/spaceranger_mkfastq/spaceranger_mkfastq" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/nextflow/demux/spaceranger_mkfastq/main.nf b/target/nextflow/demux/spaceranger_mkfastq/main.nf index d87bdda7..6b3760ea 100644 --- a/target/nextflow/demux/spaceranger_mkfastq/main.nf +++ b/target/nextflow/demux/spaceranger_mkfastq/main.nf @@ -123,7 +123,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "config" : "/home/runner/work/utilities/utilities/src/demux/spaceranger_mkfastq/config.vsh.yaml", "platform" : "nextflow", "viash_version" : "0.7.3", - "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b", + "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20", "git_remote" : "https://github.com/czbiohub/utilities" } }''')) diff --git a/target/nextflow/mapping/process_10x/.config.vsh.yaml b/target/nextflow/mapping/process_10x/.config.vsh.yaml index 86adfe5f..c8d50cf0 100644 --- a/target/nextflow/mapping/process_10x/.config.vsh.yaml +++ b/target/nextflow/mapping/process_10x/.config.vsh.yaml @@ -105,5 +105,5 @@ info: output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x" executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x/process_10x" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/nextflow/mapping/process_10x/main.nf b/target/nextflow/mapping/process_10x/main.nf index c5cdcc7e..20dbd798 100644 --- a/target/nextflow/mapping/process_10x/main.nf +++ b/target/nextflow/mapping/process_10x/main.nf @@ -168,7 +168,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "config" : "/home/runner/work/utilities/utilities/src/mapping/process_10x/config.vsh.yaml", "platform" : "nextflow", "viash_version" : "0.7.3", - "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b", + "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20", "git_remote" : "https://github.com/czbiohub/utilities" } }''')) diff --git a/target/nextflow/mapping/process_10x_auto/.config.vsh.yaml b/target/nextflow/mapping/process_10x_auto/.config.vsh.yaml index 056a13d2..0c7474e6 100644 --- a/target/nextflow/mapping/process_10x_auto/.config.vsh.yaml +++ b/target/nextflow/mapping/process_10x_auto/.config.vsh.yaml @@ -150,5 +150,5 @@ info: output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x_auto" executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_10x_auto/process_10x_auto" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/nextflow/mapping/process_10x_auto/main.nf b/target/nextflow/mapping/process_10x_auto/main.nf index 515973ab..30a48eba 100644 --- a/target/nextflow/mapping/process_10x_auto/main.nf +++ b/target/nextflow/mapping/process_10x_auto/main.nf @@ -208,7 +208,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "config" : "/home/runner/work/utilities/utilities/src/mapping/process_10x/auto.vsh.yaml", "platform" : "nextflow", "viash_version" : "0.7.3", - "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b", + "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20", "git_remote" : "https://github.com/czbiohub/utilities" } }''')) diff --git a/target/nextflow/mapping/process_smartseq2/.config.vsh.yaml b/target/nextflow/mapping/process_smartseq2/.config.vsh.yaml index 3b93e3cf..d7e88d09 100644 --- a/target/nextflow/mapping/process_smartseq2/.config.vsh.yaml +++ b/target/nextflow/mapping/process_smartseq2/.config.vsh.yaml @@ -146,5 +146,5 @@ info: output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2" executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2/process_smartseq2" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/nextflow/mapping/process_smartseq2/main.nf b/target/nextflow/mapping/process_smartseq2/main.nf index 1614271b..37e6421a 100644 --- a/target/nextflow/mapping/process_smartseq2/main.nf +++ b/target/nextflow/mapping/process_smartseq2/main.nf @@ -216,7 +216,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "config" : "/home/runner/work/utilities/utilities/src/mapping/process_smartseq2/config.vsh.yaml", "platform" : "nextflow", "viash_version" : "0.7.3", - "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b", + "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20", "git_remote" : "https://github.com/czbiohub/utilities" } }''')) diff --git a/target/nextflow/mapping/process_smartseq2_auto/.config.vsh.yaml b/target/nextflow/mapping/process_smartseq2_auto/.config.vsh.yaml index 34c6366a..212111e1 100644 --- a/target/nextflow/mapping/process_smartseq2_auto/.config.vsh.yaml +++ b/target/nextflow/mapping/process_smartseq2_auto/.config.vsh.yaml @@ -153,10 +153,10 @@ functionality: \ name using the same `fastq_regex` and `sample_id_replacement`.\n * Detect cell\ \ ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n\ \ * Write the list of samples as a yaml in the output directory.\n * Map the\ - \ reads using Cell Ranger\n * Convert the Cell Ranger output to h5mu\n * Remove\ - \ ambient RNA with CellBender\n * Remove cells with less than 100 genes or 1000\ - \ reads.\n * Make the cell names unique\n * Output one h5mu file per sample\n\ - \nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n" + \ reads using Star\n * Sort counts with samtools\n * Convert to count table\ + \ with HTSeq\n * Compute QC metrics with MultiQC\n * Output one h5mu file per\ + \ sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate\ + \ pipeline.\n" status: "enabled" set_wd_to_resources_dir: false platforms: @@ -178,5 +178,5 @@ info: output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2_auto" executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/process_smartseq2_auto/process_smartseq2_auto" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/nextflow/mapping/process_smartseq2_auto/main.nf b/target/nextflow/mapping/process_smartseq2_auto/main.nf index 8c5e8b70..2c11d0be 100644 --- a/target/nextflow/mapping/process_smartseq2_auto/main.nf +++ b/target/nextflow/mapping/process_smartseq2_auto/main.nf @@ -216,7 +216,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "entrypoint" : "auto" } ], - "description" : "Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n * Look for all `*.fastq.gz` files in the `input_dir` which\n match the regular expression in `fastq_regex`.\n * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n * Write the list of samples as a yaml in the output directory.\n * Map the reads using Cell Ranger\n * Convert the Cell Ranger output to h5mu\n * Remove ambient RNA with CellBender\n * Remove cells with less than 100 genes or 1000 reads.\n * Make the cell names unique\n * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n", + "description" : "Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n * Look for all `*.fastq.gz` files in the `input_dir` which\n match the regular expression in `fastq_regex`.\n * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n * Write the list of samples as a yaml in the output directory.\n * Map the reads using Star\n * Sort counts with samtools\n * Convert to count table with HTSeq\n * Compute QC metrics with MultiQC\n * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n", "status" : "enabled", "set_wd_to_resources_dir" : false }, @@ -242,7 +242,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "config" : "/home/runner/work/utilities/utilities/src/mapping/process_smartseq2/auto.vsh.yaml", "platform" : "nextflow", "viash_version" : "0.7.3", - "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b", + "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20", "git_remote" : "https://github.com/czbiohub/utilities" } }''')) diff --git a/target/nextflow/mapping/process_smartseq2_auto/nextflow.config b/target/nextflow/mapping/process_smartseq2_auto/nextflow.config index 8531f9aa..a3ba620b 100644 --- a/target/nextflow/mapping/process_smartseq2_auto/nextflow.config +++ b/target/nextflow/mapping/process_smartseq2_auto/nextflow.config @@ -3,6 +3,6 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' version = '0.1.1' - description = 'Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n * Look for all `*.fastq.gz` files in the `input_dir` which\n match the regular expression in `fastq_regex`.\n * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n * Write the list of samples as a yaml in the output directory.\n * Map the reads using Cell Ranger\n * Convert the Cell Ranger output to h5mu\n * Remove ambient RNA with CellBender\n * Remove cells with less than 100 genes or 1000 reads.\n * Make the cell names unique\n * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n' + description = 'Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n * Look for all `*.fastq.gz` files in the `input_dir` which\n match the regular expression in `fastq_regex`.\n * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n * Write the list of samples as a yaml in the output directory.\n * Map the reads using Star\n * Sort counts with samtools\n * Convert to count table with HTSeq\n * Compute QC metrics with MultiQC\n * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n' author = 'Angela Pisco, Robrecht Cannoodt' } \ No newline at end of file diff --git a/target/nextflow/mapping/process_smartseq2_auto/nextflow_schema.json b/target/nextflow/mapping/process_smartseq2_auto/nextflow_schema.json index dce6ccb1..5c851655 100644 --- a/target/nextflow/mapping/process_smartseq2_auto/nextflow_schema.json +++ b/target/nextflow/mapping/process_smartseq2_auto/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", "title": "process_smartseq2_auto", - "description": "Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n * Look for all `*.fastq.gz` files in the `input_dir` which\n match the regular expression in `fastq_regex`.\n * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n * Write the list of samples as a yaml in the output directory.\n * Map the reads using Cell Ranger\n * Convert the Cell Ranger output to h5mu\n * Remove ambient RNA with CellBender\n * Remove cells with less than 100 genes or 1000 reads.\n * Make the cell names unique\n * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n", + "description": "Map all SmartSeq2 Fastq files in a directory.\n\nSteps in the workflow:\n\n * Look for all `*.fastq.gz` files in the `input_dir` which\n match the regular expression in `fastq_regex`.\n * Extract the sample id from the path name using the same `fastq_regex` and `sample_id_replacement`.\n * Detect cell ids from the path name using the `fastq_regex` and `cell_id_replacement`.\n * Write the list of samples as a yaml in the output directory.\n * Map the reads using Star\n * Sort counts with samtools\n * Convert to count table with HTSeq\n * Compute QC metrics with MultiQC\n * Output one h5mu file per sample\n\nConcatenating the invididual h5mu files into one h5mu file is a separate pipeline.\n", "type": "object", "definitions": { "input directory" : { diff --git a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml index 5e835925..cb7a0a19 100644 --- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml @@ -129,5 +129,5 @@ info: output: "/home/runner/work/utilities/utilities/target/nextflow/mapping/spaceranger_count" executable: "/home/runner/work/utilities/utilities/target/nextflow/mapping/spaceranger_count/spaceranger_count" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/nextflow/mapping/spaceranger_count/main.nf b/target/nextflow/mapping/spaceranger_count/main.nf index a1cc8cdb..4832524c 100644 --- a/target/nextflow/mapping/spaceranger_count/main.nf +++ b/target/nextflow/mapping/spaceranger_count/main.nf @@ -187,7 +187,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "config" : "/home/runner/work/utilities/utilities/src/mapping/spaceranger_count/config.vsh.yaml", "platform" : "nextflow", "viash_version" : "0.7.3", - "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b", + "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20", "git_remote" : "https://github.com/czbiohub/utilities" } }''')) diff --git a/target/nextflow/tabula_sapiens/concat/.config.vsh.yaml b/target/nextflow/tabula_sapiens/concat/.config.vsh.yaml index 3ef0e44b..d9bd1c52 100644 --- a/target/nextflow/tabula_sapiens/concat/.config.vsh.yaml +++ b/target/nextflow/tabula_sapiens/concat/.config.vsh.yaml @@ -92,5 +92,5 @@ info: output: "/home/runner/work/utilities/utilities/target/nextflow/tabula_sapiens/concat" executable: "/home/runner/work/utilities/utilities/target/nextflow/tabula_sapiens/concat/concat" viash_version: "0.7.3" - git_commit: "f4bc99bf82a915a68541bcfd58b146064c8dba2b" + git_commit: "f639468c9d0ed115776e10d0f7a3330fff04ab20" git_remote: "https://github.com/czbiohub/utilities" diff --git a/target/nextflow/tabula_sapiens/concat/main.nf b/target/nextflow/tabula_sapiens/concat/main.nf index 9652f0ea..e0f35108 100644 --- a/target/nextflow/tabula_sapiens/concat/main.nf +++ b/target/nextflow/tabula_sapiens/concat/main.nf @@ -156,7 +156,7 @@ thisConfig = processConfig(jsonSlurper.parseText('''{ "config" : "/home/runner/work/utilities/utilities/src/tabula_sapiens/concat/config.vsh.yaml", "platform" : "nextflow", "viash_version" : "0.7.3", - "git_commit" : "f4bc99bf82a915a68541bcfd58b146064c8dba2b", + "git_commit" : "f639468c9d0ed115776e10d0f7a3330fff04ab20", "git_remote" : "https://github.com/czbiohub/utilities" } }'''))