From e5a3fd36eed2ca1909e971222b8117a134a61b20 Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 21 Feb 2025 11:49:43 +0000 Subject: [PATCH] Build branch main with version main (bd5b2d4) Build pipeline: viash-hub.htrnaseq.main-l2658 Source commit: https://github.com/viash-hub/htrnaseq/commit/bd5b2d41718677ee367d3829447241df9733c8d3 Source message: Keep contents for barcodes with no mapped reads. (#44) --- CHANGELOG.md | 13 +++ src/eset/create_eset/script.R | 3 +- src/eset/create_eset/test.R | 58 +++++++++++- .../EMPTY/Solo.out/Gene/raw/barcodes.tsv | 1 + .../EMPTY/Solo.out/Gene/raw/features.tsv | 25 +++++ .../EMPTY/Solo.out/Gene/raw/matrix.mtx | 3 + src/stats/generate_pool_statistics/script.py | 22 +++-- src/stats/generate_pool_statistics/test.py | 91 ++++++++++++++----- src/stats/generate_well_statistics/script.py | 1 + src/stats/generate_well_statistics/test.py | 6 +- src/workflows/htrnaseq/config.vsh.yaml | 3 + src/workflows/htrnaseq/integration_test.sh | 12 +++ src/workflows/htrnaseq/test.nf | 25 +++++ .../eset/create_eset/.config.vsh.yaml | 2 +- .../executable/eset/create_eset/create_eset | 7 +- .../eset/create_fdata/.config.vsh.yaml | 2 +- .../executable/eset/create_fdata/create_fdata | 4 +- .../eset/create_pdata/.config.vsh.yaml | 2 +- .../executable/eset/create_pdata/create_pdata | 4 +- .../htrnaseq/check_eset/.config.vsh.yaml | 2 +- .../htrnaseq/check_eset/check_eset | 4 +- .../check_cutadapt_output/.config.vsh.yaml | 2 +- .../check_cutadapt_output | 4 +- .../io/publish_fastqs/.config.vsh.yaml | 2 +- .../io/publish_fastqs/publish_fastqs | 4 +- .../io/publish_results/.config.vsh.yaml | 2 +- .../io/publish_results/publish_results | 4 +- .../executable/parallel_map/.config.vsh.yaml | 2 +- target/executable/parallel_map/parallel_map | 4 +- .../report/create_report/.config.vsh.yaml | 2 +- .../report/create_report/create_report | 4 +- .../stats/combine_star_logs/.config.vsh.yaml | 2 +- .../stats/combine_star_logs/combine_star_logs | 4 +- .../generate_pool_statistics/.config.vsh.yaml | 2 +- .../generate_pool_statistics | 26 ++++-- .../generate_well_statistics/.config.vsh.yaml | 2 +- .../generate_well_statistics | 5 +- .../eset/create_eset/.config.vsh.yaml | 2 +- target/nextflow/eset/create_eset/main.nf | 5 +- .../eset/create_fdata/.config.vsh.yaml | 2 +- target/nextflow/eset/create_fdata/main.nf | 2 +- .../eset/create_pdata/.config.vsh.yaml | 2 +- target/nextflow/eset/create_pdata/main.nf | 2 +- .../htrnaseq/check_eset/.config.vsh.yaml | 2 +- .../htrnaseq/check_eset/main.nf | 2 +- .../check_cutadapt_output/.config.vsh.yaml | 2 +- .../check_cutadapt_output/main.nf | 2 +- .../io/publish_fastqs/.config.vsh.yaml | 2 +- target/nextflow/io/publish_fastqs/main.nf | 2 +- .../io/publish_results/.config.vsh.yaml | 2 +- target/nextflow/io/publish_results/main.nf | 2 +- target/nextflow/parallel_map/.config.vsh.yaml | 2 +- target/nextflow/parallel_map/main.nf | 2 +- .../report/create_report/.config.vsh.yaml | 2 +- target/nextflow/report/create_report/main.nf | 2 +- .../stats/combine_star_logs/.config.vsh.yaml | 2 +- .../nextflow/stats/combine_star_logs/main.nf | 2 +- .../generate_pool_statistics/.config.vsh.yaml | 2 +- .../stats/generate_pool_statistics/main.nf | 24 +++-- .../generate_well_statistics/.config.vsh.yaml | 2 +- .../stats/generate_well_statistics/main.nf | 3 +- .../utils/listInputDir/.config.vsh.yaml | 2 +- target/nextflow/utils/listInputDir/main.nf | 2 +- .../workflows/htrnaseq/.config.vsh.yaml | 6 +- target/nextflow/workflows/htrnaseq/main.nf | 8 +- .../workflows/runner/.config.vsh.yaml | 2 +- target/nextflow/workflows/runner/main.nf | 2 +- .../well_demultiplex/.config.vsh.yaml | 2 +- .../workflows/well_demultiplex/main.nf | 2 +- .../workflows/well_metadata/.config.vsh.yaml | 2 +- .../nextflow/workflows/well_metadata/main.nf | 2 +- 71 files changed, 340 insertions(+), 125 deletions(-) create mode 100644 src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/barcodes.tsv create mode 100644 src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/features.tsv create mode 100644 src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/matrix.mtx diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f9e6225..03041c1c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,16 @@ +# htrnaseq v0.5.4 + +* Fix missing barcodes in the output from `generate_pool_statistics`, which caused an assertion error in `create_pdata`. + In order to resolve the issue `generate_well_statistics` now outputs results for all chromosomes/scaffolds presented by + the genome annotation, even when no reads were mapped to the regions in question. `generate_pool_statistics` will now + remove regions from the output that have not at least one counts across all barcodes (PR #44). + +# htrnaseq v0.5.3 + +## Bug fixes + +* Fix `create_eset` component failing to create when one of the input samples has no counts (PR #43). + # htrnaseq v0.5.2 ## Bug fixes diff --git a/src/eset/create_eset/script.R b/src/eset/create_eset/script.R index 9e55d22c..bab5d6d4 100644 --- a/src/eset/create_eset/script.R +++ b/src/eset/create_eset/script.R @@ -209,7 +209,6 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths, output, measure, col_names, cell_barcodes) { read_matrix <- Read10X(data_dir = exprs_file_paths, gene_column = 1) - read_matrix <- read_matrix[, which(colSums(read_matrix) != 0)] # keep index of feature names containing "_" because Seurat #changes them to "-" and they no longer match with fdata[, "gene_id"] idx <- grep("_", rownames(read_matrix)) @@ -378,7 +377,7 @@ create_eset <- function(feature_annotation_path, featureData = fdata_eset, annotation = additional_info) - + eset <- eset[, colSums(exprs(eset)) != 0] saveRDS(eset, file = output_path) message(paste0("eset created succesfully for ", ncol(eset), diff --git a/src/eset/create_eset/test.R b/src/eset/create_eset/test.R index 53d825d0..bc0b5ce5 100644 --- a/src/eset/create_eset/test.R +++ b/src/eset/create_eset/test.R @@ -73,4 +73,60 @@ input_f_data <- read.table(file.path(meta$resources_dir, "fData.tsv"), input_f_data <- input_f_data[input_f_data$gene_id %in% expected_feature_names, ] row.names(input_f_data) <- input_f_data$gene_id input_f_data[] <- lapply(input_f_data, as.character) -stopifnot(identical(input_f_data, fData(result))) \ No newline at end of file +stopifnot(identical(input_f_data, fData(result))) + +# Check results filtering of barcodes with no reads +out <- processx::run(meta$executable, c( + "--pDataFile", file.path(meta$resources_dir, "pData.tsv"), + "--fDataFile", file.path(meta$resources_dir, "fData.tsv"), + "--mappingDir", file.path(meta$resources_dir, "mapping_dir", "AACAAGGTAC"), + "--mappingDir", file.path(meta$resources_dir, "mapping_dir", "EMPTY"), + "--poolName", "bar", + "--output", output +)) +expect_equal(out$status, 0) +expect_true(file.exists(output)) +result <- readRDS(output) +stopifnot(length(sampleNames(result)) == 1) +stopifnot(all(sampleNames(result) == c("bar_AACAAGGTAC"))) +expected_feature_names <- c( + "ENS0001058", "ENS0000221", "ENS0001387", "ENS0000508", "ENS0001199", + "ENS0000477", "ENS0001457", "ENS0001040", "ENS0000114", "ENS0000821", + "ENS0001429", "ENS0001396", "ENS0000355", "ENS0000122", "ENS0000441", + "ENS0001223", "ENS0001431", "ENS0000042", "ENS0000443", "ENS0000389", + "ENS0001208", "ENS0001140", "ENS0000071", "ENS0001369" +) +stopifnot(length(featureNames(result)) == 24) +stopifnot(all(featureNames(result) == expected_feature_names)) +expected_expressions <- matrix( + c(0, + 0, + 0, + 0, + 1, + 0, + 0, + 0, + 2, + 0, + 0, + 8, + 0, + 1, + 2, + 0, + 0, + 0, + 1, + 0, + 16, + 0, + 12, + 5), + ncol = 1, + nrow = 24, + byrow = TRUE, +) +rownames(expected_expressions) <- expected_feature_names +colnames(expected_expressions) <- c("bar_AACAAGGTAC") +stopifnot(identical(exprs(result), expected_expressions)) \ No newline at end of file diff --git a/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/barcodes.tsv b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/barcodes.tsv new file mode 100644 index 00000000..ac50a9e8 --- /dev/null +++ b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/barcodes.tsv @@ -0,0 +1 @@ +CCCCCCCCCC diff --git a/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/features.tsv b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/features.tsv new file mode 100644 index 00000000..ca5527cf --- /dev/null +++ b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/features.tsv @@ -0,0 +1,25 @@ +ENS0001140 209E3 Gene Expression +ENS0001058 A2B9A Gene Expression +ENS0000508 CF168 Gene Expression +ENS0001457 3BA5A Gene Expression +ENS0001431 1C968 Gene Expression +ENS0000821 E5192 Gene Expression +ENS0001040 1821B Gene Expression +ENS0000443 5AD11 Gene Expression +ENS0000441 3F0FF Gene Expression +ENS0001387 265F2 Gene Expression +ENS0001223 28A43 Gene Expression +ENS0001208 58E28 Gene Expression +ENS0001396 6E614 Gene Expression +ENS0001199 EA941 Gene Expression +ENS0001369 99DDC Gene Expression +ENS0000770 AFCC0 Gene Expression +ENS0000389 B58E5 Gene Expression +ENS0000071 7A6C3 Gene Expression +ENS0000114 65424 Gene Expression +ENS0000355 077A2 Gene Expression +ENS0001429 22A4F Gene Expression +ENS0000477 981E6 Gene Expression +ENS0000042 E2D99 Gene Expression +ENS0000122 D90E9 Gene Expression +ENS0000221 97B0F Gene Expression \ No newline at end of file diff --git a/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/matrix.mtx b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/matrix.mtx new file mode 100644 index 00000000..107afd81 --- /dev/null +++ b/src/eset/create_eset/test_data/mapping_dir/EMPTY/Solo.out/Gene/raw/matrix.mtx @@ -0,0 +1,3 @@ +%%MatrixMarket matrix coordinate integer general +% +25 1 0 \ No newline at end of file diff --git a/src/stats/generate_pool_statistics/script.py b/src/stats/generate_pool_statistics/script.py index 48f68845..e6b57ca4 100644 --- a/src/stats/generate_pool_statistics/script.py +++ b/src/stats/generate_pool_statistics/script.py @@ -1,4 +1,5 @@ import pandas as pd +from pathlib import Path import re ### VIASH START @@ -16,20 +17,25 @@ if __name__ == "__main__": # nrReadsNrGenesPerChrom file ######### nr_reads_nr_genes_wells = [] + par["nrReadsNrGenesPerChrom"] = list(map(Path, par["nrReadsNrGenesPerChrom"])) for nr_reads_nr_genes_file in par["nrReadsNrGenesPerChrom"]: - nr_reads_nr_genes_wells.append(pd.read_csv(nr_reads_nr_genes_file, - header=0, delimiter="\t", - dtype={"WellBC": pd.StringDtype(), - "WellID": pd.StringDtype(), - "Chr": pd.StringDtype(), - "NumberOfReads": pd.UInt64Dtype(), - "NumberOfGenes": pd.UInt64Dtype()})) + nr_reads_nr_gene_well = pd.read_csv(nr_reads_nr_genes_file, + header=0, delimiter="\t", + dtype={"WellBC": pd.StringDtype(), + "WellID": pd.StringDtype(), + "Chr": pd.StringDtype(), + "NumberOfReads": pd.UInt64Dtype(), + "NumberOfGenes": pd.UInt64Dtype()}) + if nr_reads_nr_gene_well.empty: + raise ValueError(f"{nr_reads_nr_genes_file.name} does not seem to contain any information!") + nr_reads_nr_genes_wells.append(nr_reads_nr_gene_well) nr_reads_nr_genes_pool = pd.concat(nr_reads_nr_genes_wells, ignore_index=True,) total_nr_reads_per_chromosome = nr_reads_nr_genes_pool.pivot_table(index=INDEX_COL, columns="Chr", values=["NumberOfReads"], fill_value=0, aggfunc="sum").droplevel(0, axis=1) total_nr_reads_per_chromosome.columns.name = None - + # Remove scaffolds/chromosomes with no counts + total_nr_reads_per_chromosome = total_nr_reads_per_chromosome.loc[:, (total_nr_reads_per_chromosome != 0).any(axis=0)] ##### Total number of genes from all chromosomes total_nr_genes = nr_reads_nr_genes_pool.loc[:, INDEX_COL + ['NumberOfGenes']].groupby(["WellBC", "WellID"]).sum() diff --git a/src/stats/generate_pool_statistics/test.py b/src/stats/generate_pool_statistics/test.py index 6c34c2e6..7fb80b33 100644 --- a/src/stats/generate_pool_statistics/test.py +++ b/src/stats/generate_pool_statistics/test.py @@ -1,8 +1,11 @@ from uuid import uuid4 from textwrap import dedent +from subprocess import CalledProcessError import pandas as pd +import re import pytest import sys +from pathlib import Path ### VIASH START meta = { @@ -16,7 +19,7 @@ meta = { def random_path(tmp_path): def wrapper(extension=None): extension = "" if not extension else f".{extension}" - return tmp_path / f"{uuid4()}{extension}" + return Path(tmp_path / f"{uuid4()}{extension}") return wrapper @@ -181,33 +184,77 @@ def test_only_numerical_chromosomes(run_component, random_tsv_path): pd.testing.assert_frame_equal(contents, expected_frame, check_like=True) -@pytest.mark.parametrize("simple_input_file_one,expected", [("", "")], +@pytest.mark.parametrize("simple_input_file_one", [("")], indirect=["simple_input_file_one"]) -def test_one_empty_input(run_component, simple_input_file_one, expected, empty_input_file, random_tsv_path): +def test_empty_input_raises(run_component, simple_input_file_one, empty_input_file, random_tsv_path): + """ + When an input file contains no data, raise an error. + """ output_path = random_tsv_path() + with pytest.raises(CalledProcessError) as err: + run_component([ + "--nrReadsNrGenesPerChrom", simple_input_file_one, + "--nrReadsNrGenesPerChrom", empty_input_file, + "--nrReadsNrGenesPerChromPool", output_path + ]) + assert re.search( + rf"{empty_input_file.name} does not seem to contain any information", + err.value.stdout.decode("utf-8"), + ) + +def test_remove_chromosomes_with_no_counts(run_component, random_tsv_path): + """ + If a chromosome has no counts across all of the wells, it should + not be included in the output + """ + output_path = random_tsv_path() + contents1 = dedent( + f"""\ + WellBC WellID Chr NumberOfReads NumberOfGenes + CCC B2 2 2 1 + CCC B2 3 3 2 + CCC B2 5 4 2 + CCC B2 1 4 2 + CCC B2 empty 0 0 + """) + input_file_1 = random_tsv_path() + with input_file_1.open("w") as open_file: + open_file.write(contents1) + + contents2 = dedent( + f"""\ + WellBC WellID Chr NumberOfReads NumberOfGenes + AGG A1 2 2 1 + AGG A1 3 3 2 + AGG A1 5 4 2 + AGG A1 1 4 2 + AGG A1 empty 0 0 + """) + input_file_2 = random_tsv_path() + with input_file_2.open("w") as open_file: + open_file.write(contents2) + output_path = random_tsv_path() run_component([ - "--nrReadsNrGenesPerChrom", simple_input_file_one, - "--nrReadsNrGenesPerChrom", empty_input_file, + "--nrReadsNrGenesPerChrom", input_file_1, + "--nrReadsNrGenesPerChrom", input_file_2, "--nrReadsNrGenesPerChromPool", output_path ]) + # Here, the chromosome called "empty" should not be included expected_dict = { - "WellBC": ["AGG"], - "WellID": ["A1"], - f"{expected}1": ["2"], - f"{expected}2": ["3"], - f"{expected}3": ["4"], - "ERCC-1": ["1"], - "ERCC-2": ["1"], - "MT": ["4"], - f"{expected}X": ["2"], - "pctChrom": ["52.94"], - "pctMT": ["23.53"], - "pctERCC": ["11.76"], - "SumReads": ["17"], - "NumberOfGenes": ["12"], - "NumberOfERCCReads": ["2"], - "NumberOfChromReads": ["9"], - "NumberOfMTReads": ["4"], + "WellBC": ["AGG", "CCC"], + "WellID": ["A1", "B2"], + "1": ["4", "4"], + "2": ["2", "2"], + "3": ["3", "3"], + "5": ["4", "4"], + "pctChrom": ["100", "100"], + "pctMT": ["0", "0"], + "pctERCC": ["0", "0"], + "SumReads": ["13", "13"], + "NumberOfGenes": ["7", "7"], + "NumberOfERCCReads": ["0", "0"], + "NumberOfChromReads": ["13", "13"], + "NumberOfMTReads": ["0", "0"], } expected_frame = pd.DataFrame.from_dict(expected_dict, dtype=pd.StringDtype()) diff --git a/src/stats/generate_well_statistics/script.py b/src/stats/generate_well_statistics/script.py index 5bad3201..90a8397d 100644 --- a/src/stats/generate_well_statistics/script.py +++ b/src/stats/generate_well_statistics/script.py @@ -53,6 +53,7 @@ if __name__ == "__main__": NumberOfReads=pd.NamedAgg("GX", aggfunc="size"), NumberOfGenes=pd.NamedAgg(column="GX", aggfunc="nunique") ) + nr_reads_nr_genes = nr_reads_nr_genes.reindex(samfile.header.references, fill_value=0) logger.info("Done calculating number of reads per gene and per chromesome. Writing to %s", par['nrReadsNrGenesPerChrom']) nr_reads_nr_genes.reset_index(names="Chr").assign(WellBC=par["barcode"], WellID=par["well_id"])\ diff --git a/src/stats/generate_well_statistics/test.py b/src/stats/generate_well_statistics/test.py index 36f6edc9..70b770c5 100644 --- a/src/stats/generate_well_statistics/test.py +++ b/src/stats/generate_well_statistics/test.py @@ -114,8 +114,8 @@ def test_generate_well_statistics_simple_bam(run_component, input_sam_path, sam_ def test_empty_sam(run_component, empty_sam_path, sam_to_bam, random_path): """ - Test an empty bam file - Ran into issue https://github.com/pandas-dev/pandas/pull/59258 + Test an empty bam file. Make sure that chromosomes with mapped reads + are still represented. Ran into issue https://github.com/pandas-dev/pandas/pull/59258 """ bam_file = sam_to_bam(empty_sam_path) processed_bam = random_path("tsv") @@ -143,6 +143,8 @@ def test_empty_sam(run_component, empty_sam_path, sam_to_bam, random_path): expected_reads_per_chromosome = \ dedent("""\ WellBC WellID Chr NumberOfReads NumberOfGenes + ACGT A1 1 0 0 + ACGT A1 2 0 0 """) expected_nr_reads_nr_umis_per_cb = \ diff --git a/src/workflows/htrnaseq/config.vsh.yaml b/src/workflows/htrnaseq/config.vsh.yaml index 26eebe97..cf99c45f 100644 --- a/src/workflows/htrnaseq/config.vsh.yaml +++ b/src/workflows/htrnaseq/config.vsh.yaml @@ -96,6 +96,9 @@ test_resources: - type: nextflow_script path: test.nf entrypoint: test_wf + - type: nextflow_script + path: test.nf + entrypoint: test_wf2 dependencies: - name: stats/combine_star_logs repository: local diff --git a/src/workflows/htrnaseq/integration_test.sh b/src/workflows/htrnaseq/integration_test.sh index a5f68e1b..28490902 100755 --- a/src/workflows/htrnaseq/integration_test.sh +++ b/src/workflows/htrnaseq/integration_test.sh @@ -11,6 +11,8 @@ viash ns build --setup cb --parallel export NXF_VER=24.04.4 +set -eo pipefail + nextflow \ run . \ -main-script src/workflows/htrnaseq/test.nf \ @@ -19,3 +21,13 @@ nextflow \ -resume \ -profile docker,local \ --publish_dir output + +nextflow \ + run . \ + -main-script src/workflows/htrnaseq/test.nf \ + -config ./src/config/labels.config \ + -entry test_wf2 \ + -resume \ + -profile docker,local \ + --publish_dir output2 + diff --git a/src/workflows/htrnaseq/test.nf b/src/workflows/htrnaseq/test.nf index 808f1bed..24808ed0 100644 --- a/src/workflows/htrnaseq/test.nf +++ b/src/workflows/htrnaseq/test.nf @@ -43,3 +43,28 @@ workflow test_wf { ] ) } + + +workflow test_wf2 { + // Test the edge case where one of the barcodes has no reads + resources_test_file = file(params.resources_test) + input_ch = Channel.fromList([ + [ + id: "sample_one", + input_r1: resources_test_file.resolve("100k/SRR14730301/VH02001612_S9_R1_001.fastq"), + input_r2: resources_test_file.resolve("100k/SRR14730301/VH02001612_S9_R2_001.fastq"), + genomeDir: resources_test_file.resolve("genomeDir/gencode.v41.star.sparse"), + barcodesFasta: resources_test_file.resolve("2-wells-1-no-reads.fasta"), + annotation: resources_test_file.resolve("genomeDir/gencode.v41.annotation.gtf.gz") + ], + ]) + | map{ state -> [state.id, state] } + | view { "Input: $it" } + | htrnaseq.run( + toState: [ + "eset": "eset", + "star_output": "star_output", + ] + ) +} + diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 28b7bffb..eafbade3 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -198,7 +198,7 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index 82950cf2..70e2c756 100755 --- a/target/executable/eset/create_eset/create_eset +++ b/target/executable/eset/create_eset/create_eset @@ -477,9 +477,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_eset" -LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1343,7 +1343,6 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths, output, measure, col_names, cell_barcodes) { read_matrix <- Read10X(data_dir = exprs_file_paths, gene_column = 1) - read_matrix <- read_matrix[, which(colSums(read_matrix) != 0)] # keep index of feature names containing "_" because Seurat #changes them to "-" and they no longer match with fdata[, "gene_id"] idx <- grep("_", rownames(read_matrix)) @@ -1512,7 +1511,7 @@ create_eset <- function(feature_annotation_path, featureData = fdata_eset, annotation = additional_info) - + eset <- eset[, colSums(exprs(eset)) != 0] saveRDS(eset, file = output_path) message(paste0("eset created succesfully for ", ncol(eset), diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index fef05d2d..3fd42d20 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -177,7 +177,7 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index 6415a43b..553e8505 100755 --- a/target/executable/eset/create_fdata/create_fdata +++ b/target/executable/eset/create_fdata/create_fdata @@ -478,9 +478,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata" -LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 1d655091..3628193b 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -191,7 +191,7 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index c79947f7..d7cefe0b 100755 --- a/target/executable/eset/create_pdata/create_pdata +++ b/target/executable/eset/create_pdata/create_pdata @@ -488,9 +488,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata" -LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index c3167ff6..20c539d3 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -148,7 +148,7 @@ build_info: output: "target/executable/integration_test_components/htrnaseq/check_eset" executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset index eb23470f..e0ee9361 100755 --- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset +++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset @@ -470,9 +470,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset" -LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 3d64823e..a08d40d5 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -158,7 +158,7 @@ build_info: output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output index 9ae4b2af..4160480a 100755 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output @@ -476,9 +476,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output" -LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index ad8e78df..d9137e9e 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -143,7 +143,7 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index 4e030e96..48a4a51a 100755 --- a/target/executable/io/publish_fastqs/publish_fastqs +++ b/target/executable/io/publish_fastqs/publish_fastqs @@ -470,9 +470,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs" -LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:28Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index 11361da6..f9f02c0f 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index 97e32679..d2524ca4 100755 --- a/target/executable/io/publish_results/publish_results +++ b/target/executable/io/publish_results/publish_results @@ -484,9 +484,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_results" -LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:29Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 3f8b8c2e..edbedc4e 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -279,7 +279,7 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index 9ba57e27..ad541074 100755 --- a/target/executable/parallel_map/parallel_map +++ b/target/executable/parallel_map/parallel_map @@ -540,9 +540,9 @@ ENV STAR_BINARY=STAR COPY STAR /usr/local/bin/$STAR_BINARY LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component parallel_map" -LABEL org.opencontainers.image.created="2025-02-17T14:58:43Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index dd7de1de..f2b01287 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -201,7 +201,7 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index 8ef3ff66..92e75635 100755 --- a/target/executable/report/create_report/create_report +++ b/target/executable/report/create_report/create_report @@ -476,9 +476,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component report create_report" -LABEL org.opencontainers.image.created="2025-02-17T14:58:43Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index 770d8e91..ed52e61d 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -198,7 +198,7 @@ build_info: output: "target/executable/stats/combine_star_logs" executable: "target/executable/stats/combine_star_logs/combine_star_logs" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index 1b82a0fe..1fbaf5d5 100755 --- a/target/executable/stats/combine_star_logs/combine_star_logs +++ b/target/executable/stats/combine_star_logs/combine_star_logs @@ -490,9 +490,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs" -LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:28Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index 0f9a631a..d47f16dd 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -182,7 +182,7 @@ build_info: output: "target/executable/stats/generate_pool_statistics" executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index 4c035407..6c2f2174 100755 --- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics +++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics @@ -483,9 +483,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics" -LABEL org.opencontainers.image.created="2025-02-17T14:58:41Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:29Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1044,6 +1044,7 @@ trap clean_up EXIT trap interrupt INT SIGINT cat > "\$tempscript" << 'VIASHMAIN' import pandas as pd +from pathlib import Path import re ### VIASH START @@ -1085,20 +1086,25 @@ if __name__ == "__main__": # nrReadsNrGenesPerChrom file ######### nr_reads_nr_genes_wells = [] + par["nrReadsNrGenesPerChrom"] = list(map(Path, par["nrReadsNrGenesPerChrom"])) for nr_reads_nr_genes_file in par["nrReadsNrGenesPerChrom"]: - nr_reads_nr_genes_wells.append(pd.read_csv(nr_reads_nr_genes_file, - header=0, delimiter="\\t", - dtype={"WellBC": pd.StringDtype(), - "WellID": pd.StringDtype(), - "Chr": pd.StringDtype(), - "NumberOfReads": pd.UInt64Dtype(), - "NumberOfGenes": pd.UInt64Dtype()})) + nr_reads_nr_gene_well = pd.read_csv(nr_reads_nr_genes_file, + header=0, delimiter="\\t", + dtype={"WellBC": pd.StringDtype(), + "WellID": pd.StringDtype(), + "Chr": pd.StringDtype(), + "NumberOfReads": pd.UInt64Dtype(), + "NumberOfGenes": pd.UInt64Dtype()}) + if nr_reads_nr_gene_well.empty: + raise ValueError(f"{nr_reads_nr_genes_file.name} does not seem to contain any information!") + nr_reads_nr_genes_wells.append(nr_reads_nr_gene_well) nr_reads_nr_genes_pool = pd.concat(nr_reads_nr_genes_wells, ignore_index=True,) total_nr_reads_per_chromosome = nr_reads_nr_genes_pool.pivot_table(index=INDEX_COL, columns="Chr", values=["NumberOfReads"], fill_value=0, aggfunc="sum").droplevel(0, axis=1) total_nr_reads_per_chromosome.columns.name = None - + # Remove scaffolds/chromosomes with no counts + total_nr_reads_per_chromosome = total_nr_reads_per_chromosome.loc[:, (total_nr_reads_per_chromosome != 0).any(axis=0)] ##### Total number of genes from all chromosomes total_nr_genes = nr_reads_nr_genes_pool.loc[:, INDEX_COL + ['NumberOfGenes']].groupby(["WellBC", "WellID"]).sum() diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index c77dc585..0c5e9b45 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -264,7 +264,7 @@ build_info: output: "target/executable/stats/generate_well_statistics" executable: "target/executable/stats/generate_well_statistics/generate_well_statistics" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index 81d59c6b..c18f920d 100755 --- a/target/executable/stats/generate_well_statistics/generate_well_statistics +++ b/target/executable/stats/generate_well_statistics/generate_well_statistics @@ -520,9 +520,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics" -LABEL org.opencontainers.image.created="2025-02-17T14:58:42Z" +LABEL org.opencontainers.image.created="2025-02-21T11:03:29Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="3c05b7950b9627acdaa70687e0915d5ee69b6d1b" +LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3" LABEL org.opencontainers.image.version="main" VIASHDOCKER @@ -1259,6 +1259,7 @@ if __name__ == "__main__": NumberOfReads=pd.NamedAgg("GX", aggfunc="size"), NumberOfGenes=pd.NamedAgg(column="GX", aggfunc="nunique") ) + nr_reads_nr_genes = nr_reads_nr_genes.reindex(samfile.header.references, fill_value=0) logger.info("Done calculating number of reads per gene and per chromesome. Writing to %s", par['nrReadsNrGenesPerChrom']) nr_reads_nr_genes.reset_index(names="Chr").assign(WellBC=par["barcode"], WellID=par["well_id"])\\ diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index 95a49e0a..539bdd9d 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -198,7 +198,7 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index f6ce18c3..be985081 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -3072,7 +3072,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3365,7 +3365,6 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths, output, measure, col_names, cell_barcodes) { read_matrix <- Read10X(data_dir = exprs_file_paths, gene_column = 1) - read_matrix <- read_matrix[, which(colSums(read_matrix) != 0)] # keep index of feature names containing "_" because Seurat #changes them to "-" and they no longer match with fdata[, "gene_id"] idx <- grep("_", rownames(read_matrix)) @@ -3534,7 +3533,7 @@ create_eset <- function(feature_annotation_path, featureData = fdata_eset, annotation = additional_info) - + eset <- eset[, colSums(exprs(eset)) != 0] saveRDS(eset, file = output_path) message(paste0("eset created succesfully for ", ncol(eset), diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml index 0c756600..8d86a8eb 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -177,7 +177,7 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index 7d6255ad..94c29bfb 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -3044,7 +3044,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml index 2f48aa57..dce2045b 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -191,7 +191,7 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index 74daa2c7..8566e68b 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -3058,7 +3058,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index e7c718e1..115b925b 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -148,7 +148,7 @@ build_info: output: "target/nextflow/integration_test_components/htrnaseq/check_eset" executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf index cca1aecf..acf23948 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -2997,7 +2997,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 88365a32..39435918 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -158,7 +158,7 @@ build_info: output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf index cf983be1..4812a63b 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf @@ -3009,7 +3009,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml index 9d2aefdd..f392b242 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -143,7 +143,7 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index a3edb19b..e7ec8fd7 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -2983,7 +2983,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml index 9ff1dd14..5093826c 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -187,7 +187,7 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index 3365a69d..25a7e421 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -3032,7 +3032,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index 2a693c35..50cfb3c6 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -279,7 +279,7 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index 5d63df86..aa74972a 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -3144,7 +3144,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml index 960f0882..eeea0566 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -201,7 +201,7 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index 36b0d02f..9ee0263b 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -3077,7 +3077,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml index f8d96050..0481b4ac 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -198,7 +198,7 @@ build_info: output: "target/nextflow/stats/combine_star_logs" executable: "target/nextflow/stats/combine_star_logs/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index 5093edc0..d03b62c1 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -3060,7 +3060,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml index 04971d6b..c12a9fc5 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -182,7 +182,7 @@ build_info: output: "target/nextflow/stats/generate_pool_statistics" executable: "target/nextflow/stats/generate_pool_statistics/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index d714a631..047d08e9 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -3044,7 +3044,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3096,6 +3096,7 @@ def innerWorkflowFactory(args) { tempscript=".viash_script.sh" cat > "$tempscript" << VIASHMAIN import pandas as pd +from pathlib import Path import re ### VIASH START @@ -3137,20 +3138,25 @@ if __name__ == "__main__": # nrReadsNrGenesPerChrom file ######### nr_reads_nr_genes_wells = [] + par["nrReadsNrGenesPerChrom"] = list(map(Path, par["nrReadsNrGenesPerChrom"])) for nr_reads_nr_genes_file in par["nrReadsNrGenesPerChrom"]: - nr_reads_nr_genes_wells.append(pd.read_csv(nr_reads_nr_genes_file, - header=0, delimiter="\\\\t", - dtype={"WellBC": pd.StringDtype(), - "WellID": pd.StringDtype(), - "Chr": pd.StringDtype(), - "NumberOfReads": pd.UInt64Dtype(), - "NumberOfGenes": pd.UInt64Dtype()})) + nr_reads_nr_gene_well = pd.read_csv(nr_reads_nr_genes_file, + header=0, delimiter="\\\\t", + dtype={"WellBC": pd.StringDtype(), + "WellID": pd.StringDtype(), + "Chr": pd.StringDtype(), + "NumberOfReads": pd.UInt64Dtype(), + "NumberOfGenes": pd.UInt64Dtype()}) + if nr_reads_nr_gene_well.empty: + raise ValueError(f"{nr_reads_nr_genes_file.name} does not seem to contain any information!") + nr_reads_nr_genes_wells.append(nr_reads_nr_gene_well) nr_reads_nr_genes_pool = pd.concat(nr_reads_nr_genes_wells, ignore_index=True,) total_nr_reads_per_chromosome = nr_reads_nr_genes_pool.pivot_table(index=INDEX_COL, columns="Chr", values=["NumberOfReads"], fill_value=0, aggfunc="sum").droplevel(0, axis=1) total_nr_reads_per_chromosome.columns.name = None - + # Remove scaffolds/chromosomes with no counts + total_nr_reads_per_chromosome = total_nr_reads_per_chromosome.loc[:, (total_nr_reads_per_chromosome != 0).any(axis=0)] ##### Total number of genes from all chromosomes total_nr_genes = nr_reads_nr_genes_pool.loc[:, INDEX_COL + ['NumberOfGenes']].groupby(["WellBC", "WellID"]).sum() diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml index 05524e24..005277de 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -264,7 +264,7 @@ build_info: output: "target/nextflow/stats/generate_well_statistics" executable: "target/nextflow/stats/generate_well_statistics/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index 4c752589..b7122a23 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -3139,7 +3139,7 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { @@ -3270,6 +3270,7 @@ if __name__ == "__main__": NumberOfReads=pd.NamedAgg("GX", aggfunc="size"), NumberOfGenes=pd.NamedAgg(column="GX", aggfunc="nunique") ) + nr_reads_nr_genes = nr_reads_nr_genes.reindex(samfile.header.references, fill_value=0) logger.info("Done calculating number of reads per gene and per chromesome. Writing to %s", par['nrReadsNrGenesPerChrom']) nr_reads_nr_genes.reset_index(names="Chr").assign(WellBC=par["barcode"], WellID=par["well_id"])\\\\ diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml index 332ca4e6..24b674c2 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -165,7 +165,7 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf index 57c84277..ff80d504 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -3004,7 +3004,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index c03bf800..c82186bf 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -197,6 +197,10 @@ test_resources: path: "test.nf" is_executable: true entrypoint: "test_wf" +- type: "nextflow_script" + path: "test.nf" + is_executable: true + entrypoint: "test_wf2" info: null status: "enabled" requirements: @@ -319,7 +323,7 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/stats/combine_star_logs" diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index afa67c2b..30a188ae 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -3049,6 +3049,12 @@ meta = [ "path" : "test.nf", "is_executable" : true, "entrypoint" : "test_wf" + }, + { + "type" : "nextflow_script", + "path" : "test.nf", + "is_executable" : true, + "entrypoint" : "test_wf2" } ], "status" : "enabled", @@ -3223,7 +3229,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index 7666d2c9..62bcee9d 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -207,7 +207,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/utils/listInputDir" diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index 2b914990..69fdb59f 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -3069,7 +3069,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 001526b7..37ea5d36 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -211,7 +211,7 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt" diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index ecec98ed..7cc04277 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -3084,7 +3084,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml index 98fc55de..3d219dd7 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -209,7 +209,7 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.0" - git_commit: "3c05b7950b9627acdaa70687e0915d5ee69b6d1b" + git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index 558fc07f..4769461e 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -3064,7 +3064,7 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.0", - "git_commit" : "3c05b7950b9627acdaa70687e0915d5ee69b6d1b", + "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : {