From 8c5a69612681e913854942a3b5971c42edac14bc Mon Sep 17 00:00:00 2001 From: fgvieira <1151762+fgvieira@users.noreply.github.com> Date: Thu, 27 Aug 2026 11:29:05 +0200 Subject: [PATCH 1/2] Small tweaks --- .../reports/multiqc_taxon.upload.log} | 0 .../.tests/unit/test_multiqc_taxon_upload.py | 2 +- pixi.lock | 580 ++++++++++-------- workflow/Snakefile | 20 +- 4 files changed, 335 insertions(+), 267 deletions(-) rename examples/euk_prok_virus/.tests/unit/multiqc_taxon_upload/expected/{stats/reports/multiqc_taxon.upload.flag => temp/reports/multiqc_taxon.upload.log} (100%) diff --git a/examples/euk_prok_virus/.tests/unit/multiqc_taxon_upload/expected/stats/reports/multiqc_taxon.upload.flag b/examples/euk_prok_virus/.tests/unit/multiqc_taxon_upload/expected/temp/reports/multiqc_taxon.upload.log similarity index 100% rename from examples/euk_prok_virus/.tests/unit/multiqc_taxon_upload/expected/stats/reports/multiqc_taxon.upload.flag rename to examples/euk_prok_virus/.tests/unit/multiqc_taxon_upload/expected/temp/reports/multiqc_taxon.upload.log diff --git a/examples/euk_prok_virus/.tests/unit/test_multiqc_taxon_upload.py b/examples/euk_prok_virus/.tests/unit/test_multiqc_taxon_upload.py index c10b505..3a46380 100644 --- a/examples/euk_prok_virus/.tests/unit/test_multiqc_taxon_upload.py +++ b/examples/euk_prok_virus/.tests/unit/test_multiqc_taxon_upload.py @@ -32,7 +32,7 @@ def test_multiqc_taxon_upload(conda_prefix): "python", "-m", "snakemake", - "stats/reports/multiqc_taxon.upload.flag", + "temp/reports/multiqc_taxon.upload.log", "--snakefile", "../../workflow/Snakefile", "-f", diff --git a/pixi.lock b/pixi.lock index 531dda2..74d41a3 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,7 +11,7 @@ environments: - https://pypi.org/simple packages: linux-64: - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.25.2-hdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-9.26.0-hdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-2.8.0-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-executor-plugin-slurm-jobstep-0.6.1-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-common-1.23.0-pyhdfd78af_1.conda @@ -22,7 +22,7 @@ environments: - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-interface-storage-plugins-4.4.1-pyh84498cf_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-logger-plugin-panoptes-0.3.0-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-logger-plugin-snkmt-0.1.8-pyhdfd78af_0.conda - - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.25.2-pyhdfd78af_0.conda + - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-minimal-9.26.0-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-fs-1.1.3-pyhdfd78af_0.conda - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-ftp-0.1.3-pyhdfd78af_0.tar.bz2 - conda: https://conda.anaconda.org/bioconda/noarch/snakemake-storage-plugin-http-0.3.1-pyhdfd78af_0.conda @@ -58,11 +58,11 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h373387f_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h280c20c_3.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.8.1-hecca717_1.conda - - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.7.0-h3435931_0.conda - 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size: 177303 - timestamp: 1786443183227 + size: 177981 + timestamp: 1787739748442 - conda: https://conda.anaconda.org/conda-forge/noarch/h11-0.16.0-pyhcf101f3_1.conda sha256: 96cac6573fd35ae151f4d6979bab6fbc90cb6b1fb99054ba19eb075da9822fcb md5: b8993c19b0c32a2f7b66cbb58ca27069 @@ -4852,9 +4921,9 @@ packages: run_exports: {} size: 120685 timestamp: 1764517220861 -- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_0.conda - sha256: db973a37d75db8e19b5f44bbbdaead0c68dde745407f281e2a7fe4db74ec51d7 - md5: ada41c863af263cc4c5fcbaff7c3e4dc +- conda: https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.26.0-pyhcf101f3_1.conda + sha256: 328756a4555941d57af4a5f553e5d8598e9f3b37db028f557e30f9f0b3086db6 + md5: 204b5ca91eba7738790ecc333facbbbe depends: - attrs >=22.2.0 - jsonschema-specifications >=2023.3.6 @@ -4865,10 +4934,10 @@ packages: license: MIT license_family: MIT purls: - - pkg:pypi/jsonschema?source=hash-mapping + - pkg:pypi/jsonschema?source=compressed-mapping run_exports: {} - 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size: 26062 - timestamp: 1772476821244 + size: 26632 + timestamp: 1787667852023 - conda: https://conda.anaconda.org/conda-forge/noarch/logmuse-0.3.0-pyhcf101f3_0.conda sha256: 36167f5a11ad1a69d24ac062f866f6abe6618eff9750d5b6efecd64b76aec759 md5: 789b0a3d1b8e7d69733894ac32eb8b69 @@ -5172,9 +5242,9 @@ packages: run_exports: {} size: 1198163 timestamp: 1785914482439 -- conda: https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.11.3-pyhcf101f3_0.conda - sha256: 810511c90649ca59fa0174958a210fd5051c0a7848cfbd42c87054a6836726b5 - md5: 31474b00d0ca5accac14eda09ba11216 +- conda: https://conda.anaconda.org/conda-forge/noarch/platformdirs-4.11.4-pyhcf101f3_0.conda + sha256: 36596d60d6bc49c4c27f009ab3128c63ea50ac5d67dffc44df05ab3d78bc4669 + md5: 840f27e0254bcdc8382ac2ca32782a22 depends: - python >=3.10 - python @@ -5183,8 +5253,8 @@ packages: purls: - pkg:pypi/platformdirs?source=compressed-mapping run_exports: {} - size: 26956 - timestamp: 1786708411066 + size: 27321 + timestamp: 1787603822584 - conda: https://conda.anaconda.org/conda-forge/noarch/pluggy-1.6.0-pyhf9edf01_1.conda sha256: e14aafa63efa0528ca99ba568eaf506eb55a0371d12e6250aaaa61718d2eb62e md5: d7585b6550ad04c8c5e21097ada2888e @@ -5376,17 +5446,17 @@ packages: run_exports: {} size: 254446 timestamp: 1786892280524 -- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.7-h4df99d1_100.conda - sha256: 05d8d9f928cf1ba1217b3cde7fb41dfe2995feb4e6b4ef5b1a9f19ce44e18f66 - md5: c56da48fd8d5d1feb1829d0241fd338c +- conda: https://conda.anaconda.org/conda-forge/noarch/python-gil-3.14.7-h4df99d1_101.conda + sha256: c39431bdbf23eff2eaa1591b438e5fd7e7db2fb635262b6eefd658dfa2f19c7c + md5: 35bb169c9d712dfc590b88f28f852157 depends: - cpython 3.14.7.* - python_abi * *_cp314 license: Python-2.0 purls: [] run_exports: {} - size: 50369 - timestamp: 1787153622440 + size: 50521 + timestamp: 1787780107541 - conda: https://conda.anaconda.org/conda-forge/noarch/python-installer-1.0.1-pyh332efcf_0.conda sha256: 9c18fa1ebd0c839b6ea12e99d510a0968c2288cc423185cb34bf7332b97684e9 md5: 5cc7e2e78962dc902cae9e29c2aa4b2f diff --git a/workflow/Snakefile b/workflow/Snakefile index 1e1e16d..fdbee61 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -87,18 +87,16 @@ from snakemake.logging import logger base_dir = Path(workflow.basedir).resolve(strict=True) repo = git.Repo(base_dir.parent) -tag_recent = [ - [tag.name, commit.hexsha] - for commit in repo.iter_commits() - for tag in repo.tags - if commit.hexsha == tag.commit.hexsha -][0] +# Latest reachable tag +tag_recent = repo.git.describe("--tags", "--abbrev=0") logger.info( "Git commit: {commit_hash} [{tag_flag}{commit_tag}] ({commit_time})".format( commit_hash=repo.head.commit.hexsha, commit_time=repo.head.commit.committed_datetime.strftime("%Y-%m-%d %H:%M:%S"), - tag_flag="" if tag_recent[1] == repo.head.commit.hexsha else ">", - commit_tag=tag_recent[0], + tag_flag=( + "" if repo.commit(tag_recent).hexsha == repo.head.commit.hexsha else ">" + ), + commit_tag=tag_recent, ) ) config_json = json.dumps(config, sort_keys=True).encode("utf-8") @@ -150,7 +148,7 @@ rule multiqc_trim_upload: rules.target_trim.input, zip=rules.multiqc_trim.output.data, output: - "stats/reports/multiqc_trim.upload.flag", + temp("temp/reports/multiqc_trim.upload.log"), log: "logs/reports/multiqc_trim.upload.log", localrule: True @@ -199,7 +197,7 @@ use rule multiqc_trim_upload as multiqc_derep_upload with: rules.target_derep.input, zip=rules.multiqc_derep.output.data, output: - touch("stats/reports/multiqc_derep.upload.flag"), + temp("temp/reports/multiqc_derep.upload.log"), log: "logs/reports/multiqc_derep.upload.log", @@ -244,6 +242,6 @@ use rule multiqc_trim_upload as multiqc_taxon_upload with: rules.target_taxon.input, zip=rules.multiqc_taxon.output.data, output: - touch("stats/reports/multiqc_taxon.upload.flag"), + temp("temp/reports/multiqc_taxon.upload.log"), log: "logs/reports/multiqc_taxon.upload.log", From 4fca39369284bc954fc3b2b56a609dc7e9ba2f0a Mon Sep 17 00:00:00 2001 From: fgvieira <1151762+fgvieira@users.noreply.github.com> Date: Thu, 27 Aug 2026 15:13:27 +0200 Subject: [PATCH 2/2] Update DAGs --- examples/euk_prok_virus/dag.svg | 2310 ++++++++++++------------- examples/euk_prok_virus/filegraph.svg | 70 +- examples/euk_prok_virus/rulegraph.svg | 72 +- 3 files changed, 1226 insertions(+), 1226 deletions(-) diff --git a/examples/euk_prok_virus/dag.svg b/examples/euk_prok_virus/dag.svg index 876bf67..2f54dcb 100644 --- a/examples/euk_prok_virus/dag.svg +++ b/examples/euk_prok_virus/dag.svg @@ -4,2345 +4,2345 @@ - + snakemake_dag - + 0 - -multiqc_taxon_upload + +multiqc_taxon_upload 1 - -multiqc_taxon + +multiqc_taxon 1->0 - - + + 2 - -trim_fastqc_raw + +trim_fastqc_raw 2->1 - - + + 3 - -trim_get_fastq_raw -lane: L001 -library: LVsim2 -read_type_raw: R2 -sample: Lib + +trim_get_fastq_raw +lane: L001 +library: LVsim1 +read_type_raw: R1 +sample: Lib 3->2 - - + + - - -15 - -trim_adapterremoval_fastq_pe + + +16 + +trim_adapterremoval_fastq_pe - - -3->15 - - + + +3->16 + + 4 - -trim_fastqc_raw + +trim_fastqc_raw 4->1 - - + + 5 - -trim_get_fastq_raw -lane: L002 -library: LVsim1 -read_type_raw: R1 -sample: Lib + +trim_get_fastq_raw +lane: L001 +library: LVsim2 +read_type_raw: R2 +sample: Lib 5->4 - - + + 14 - -trim_adapterremoval_fastq_pe + +trim_adapterremoval_fastq_pe - + 5->14 - - + + 6 - -trim_fastqc_raw + +trim_fastqc_raw 6->1 - - + + 7 - -trim_get_fastq_raw -lane: L001 -library: LVsim1 -read_type_raw: R2 -sample: Lib + +trim_get_fastq_raw +lane: L001 +library: LVsim1 +read_type_raw: R2 +sample: Lib 7->6 - - - - - -16 - -trim_adapterremoval_fastq_pe + + 7->16 - - + + 8 - -trim_fastqc_raw + +trim_fastqc_raw 8->1 - - + + 9 - -trim_get_fastq_raw -lane: L001 -library: LVsim1 -read_type_raw: R1 -sample: Lib + +trim_get_fastq_raw +lane: L002 +library: LVsim1 +read_type_raw: R1 +sample: Lib 9->8 - - + + - - -9->16 - - + + +15 + +trim_adapterremoval_fastq_pe + + + +9->15 + + 10 - -trim_fastqc_raw + +trim_fastqc_raw 10->1 - - + + 11 - -trim_get_fastq_raw -lane: L001 -library: LVsim2 -read_type_raw: R1 -sample: Lib + +trim_get_fastq_raw +lane: L002 +library: LVsim1 +read_type_raw: R2 +sample: Lib 11->10 - - + + - + 11->15 - - + + 12 - -trim_fastqc_raw + +trim_fastqc_raw 12->1 - - + + 13 - -trim_get_fastq_raw -lane: L002 -library: LVsim1 -read_type_raw: R2 -sample: Lib + +trim_get_fastq_raw +lane: L001 +library: LVsim2 +read_type_raw: R1 +sample: Lib 13->12 - - + + - + 13->14 - - + + 14->1 - - - - - -20 - -trim_fastqc_trim -read_type_trim: collapsedtrunc - - - -14->20 - - - - - -21 - -trim_fastqc_trim -read_type_trim: collapsed - - - -14->21 - - - - - -23 - -trim_fastqc_trim -read_type_trim: R2 - - - -14->23 - - + + 24 - -trim_fastqc_trim -read_type_trim: R1 + +trim_fastqc_trim +read_type_trim: singleton 14->24 - - + + 26 - -trim_fastqc_trim -read_type_trim: singleton + +trim_fastqc_trim +read_type_trim: R1 14->26 - - + + - - -33 - -derep_merge_lanes -read_type_trim: collapsed + + +29 + +trim_fastqc_trim +read_type_trim: R2 - - -14->33 - - + + +14->29 + + + + + +30 + +trim_fastqc_trim +read_type_trim: collapsedtrunc + + + +14->30 + + + + + +31 + +trim_fastqc_trim +read_type_trim: collapsed + + + +14->31 + + + + + +35 + +derep_merge_lanes +read_type_trim: collapsed + + + +14->35 + + 15->1 - - - - - -17 - -trim_fastqc_trim -read_type_trim: collapsed - - - -15->17 - - + + 19 - -trim_fastqc_trim -read_type_trim: R2 + +trim_fastqc_trim +read_type_trim: singleton 15->19 - - + + + + + +20 + +trim_fastqc_trim +read_type_trim: R2 + + + +15->20 + + + + + +21 + +trim_fastqc_trim +read_type_trim: R1 + + + +15->21 + + 22 - -trim_fastqc_trim -read_type_trim: collapsedtrunc + +trim_fastqc_trim +read_type_trim: collapsed 15->22 - - - - - -29 - -trim_fastqc_trim -read_type_trim: singleton + + - - -15->29 - - - - - -31 - -trim_fastqc_trim -read_type_trim: R1 + + +27 + +trim_fastqc_trim +read_type_trim: collapsedtrunc - - -15->31 - - + + +15->27 + + - - -35 - -derep_merge_lanes -read_type_trim: collapsed + + +33 + +derep_merge_lanes +read_type_trim: collapsed - - -15->35 - - + + +15->33 + + 16->1 - - + + + + + +17 + +trim_fastqc_trim +read_type_trim: R2 + + + +16->17 + + 18 - -trim_fastqc_trim -read_type_trim: R1 + +trim_fastqc_trim +read_type_trim: singleton 16->18 - - + + + + + +23 + +trim_fastqc_trim +read_type_trim: collapsed + + + +16->23 + + 25 - -trim_fastqc_trim -read_type_trim: R2 + +trim_fastqc_trim +read_type_trim: R1 16->25 - - - - - -27 - -trim_fastqc_trim -read_type_trim: collapsedtrunc - - - -16->27 - - + + 28 - -trim_fastqc_trim -read_type_trim: singleton + +trim_fastqc_trim +read_type_trim: collapsedtrunc 16->28 - - - - - -30 - -trim_fastqc_trim -read_type_trim: collapsed - - - -16->30 - - + + 16->33 - - + + 17->1 - - + + 18->1 - - + + 19->1 - - + + 20->1 - - + + 21->1 - - + + 22->1 - - + + 23->1 - - + + 24->1 - - + + 25->1 - - + + 26->1 - - + + 27->1 - - + + 28->1 - - + + 29->1 - - + + 30->1 - - + + 31->1 - - + + 32 - -derep_fastqc -tool: merge_lanes + +derep_fastqc +tool: merge_lanes 32->1 - - + + 33->32 - - + + - - -39 - -derep_nonpareil_infer -tool: merge_lanes + + +37 + +derep_nonpareil_infer +tool: merge_lanes - - -33->39 - - + + +33->37 + + - - -41 - -derep_seqkit + + +43 + +derep_seqkit - - -33->41 - - + + +33->43 + + 34 - -derep_fastqc -tool: merge_lanes + +derep_fastqc +tool: merge_lanes 34->1 - - + + 35->34 - - + + - - -37 - -derep_nonpareil_infer -tool: merge_lanes + + +39 + +derep_nonpareil_infer +tool: merge_lanes - - -35->37 - - + + +35->39 + + - - -43 - -derep_seqkit + + +41 + +derep_seqkit - - -35->43 - - + + +35->41 + + 36 - -derep_nonpareil_plot + +derep_nonpareil_plot 36->1 - - + + 37->36 - - + + 38 - -derep_nonpareil_plot + +derep_nonpareil_plot 38->1 - - + + 39->38 - - + + 40 - -derep_fastqc -tool: derep + +derep_fastqc +tool: derep 40->1 - - + + 41->40 - - + + 47 - -derep_low_complexity + +derep_low_complexity 41->47 - - + + 42 - -derep_fastqc -tool: derep + +derep_fastqc +tool: derep 42->1 - - + + 43->42 - - + + 45 - -derep_low_complexity + +derep_low_complexity 43->45 - - + + 44 - -derep_fastqc -tool: low_complexity + +derep_fastqc +tool: low_complexity 44->1 - - + + 45->44 - - + + - - -67 - -prefilter_reads_extract + + +49 + +prefilter_reads_extract - - -45->67 - - + + +45->49 + + - - -73 - -taxon_prefilter_shard_bowtie2 -n_shard: 1 -read_type_map: collapsed -ref: virus -tot_shards: 1 - - - -45->73 - - + + +55 + +taxon_prefilter_shard_bowtie2 +n_shard: 1 +read_type_map: collapsed +ref: virus +tot_shards: 1 + + + +45->55 + + - - -76 - -taxon_prefilter_shard_bowtie2 -n_shard: 2 -read_type_map: collapsed -ref: prok -tot_shards: 2 - - - -45->76 - - + + +59 + +taxon_prefilter_shard_bowtie2 +n_shard: 2 +read_type_map: collapsed +ref: prok +tot_shards: 2 + + + +45->59 + + - - -78 - -taxon_prefilter_shard_bowtie2 -n_shard: 1 -read_type_map: collapsed -ref: prok -tot_shards: 2 - - - -45->78 - - + + +61 + +taxon_prefilter_shard_bowtie2 +n_shard: 1 +read_type_map: collapsed +ref: prok +tot_shards: 2 + + + +45->61 + + - - -129 - -taxon_prefilter_shard_saturated_reads_extract + + +128 + +taxon_prefilter_shard_saturated_reads_extract - - -45->129 - - + + +45->128 + + - - -133 - -taxon_shard_saturated_reads_extract + + +132 + +taxon_shard_saturated_reads_extract - - -45->133 - - + + +45->132 + + 46 - -derep_fastqc -tool: low_complexity + +derep_fastqc +tool: low_complexity 46->1 - - + + 47->46 - - + + - - -49 - -prefilter_reads_extract + + +67 + +prefilter_reads_extract - - -47->49 - - + + +47->67 + + - - -55 - -taxon_prefilter_shard_bowtie2 -n_shard: 1 -read_type_map: collapsed -ref: virus -tot_shards: 1 - - - -47->55 - - + + +73 + +taxon_prefilter_shard_bowtie2 +n_shard: 1 +read_type_map: collapsed +ref: virus +tot_shards: 1 + + + +47->73 + + - - -58 - -taxon_prefilter_shard_bowtie2 -n_shard: 2 -read_type_map: collapsed -ref: prok -tot_shards: 2 - - - -47->58 - - + + +77 + +taxon_prefilter_shard_bowtie2 +n_shard: 2 +read_type_map: collapsed +ref: prok +tot_shards: 2 + + + +47->77 + + - - -60 - -taxon_prefilter_shard_bowtie2 -n_shard: 1 -read_type_map: collapsed -ref: prok -tot_shards: 2 - - - -47->60 - - + + +79 + +taxon_prefilter_shard_bowtie2 +n_shard: 1 +read_type_map: collapsed +ref: prok +tot_shards: 2 + + + +47->79 + + - - -128 - -taxon_prefilter_shard_saturated_reads_extract + + +129 + +taxon_prefilter_shard_saturated_reads_extract - - -47->128 - - + + +47->129 + + - - -132 - -taxon_shard_saturated_reads_extract + + +133 + +taxon_shard_saturated_reads_extract - - -47->132 - - + + +47->133 + + 48 - -prefilter_fastqc + +prefilter_fastqc 48->1 - - + + 49->48 - - + + 96 - -taxon_shard_bowtie2 -n_shard: 1 -ref: mitoch -tot_shards: 1 + +taxon_shard_bowtie2 +n_shard: 1 +ref: plastid +tot_shards: 1 49->96 - - + + - - -99 - -taxon_shard_bowtie2 -n_shard: 1 -ref: plastid -tot_shards: 1 + + +97 + +taxon_shard_bowtie2 +n_shard: 1 +ref: mitoch +tot_shards: 1 - - -49->99 - - + + +49->97 + + 50 - -prefilter_reads_merge + +prefilter_reads_merge 50->49 - - + + 51 - -prefilter_reads_taxonomy + +prefilter_reads_taxonomy 51->50 - - + + 52 - -taxon_prefilter_align_merge + +taxon_prefilter_align_merge 52->51 - - + + 84 - -taxon_prefilter_align_samtools_stats + +taxon_prefilter_align_samtools_stats 52->84 - - + + 87 - -taxon_prefilter_align_sort_taxon + +taxon_prefilter_align_sort_taxon 52->87 - - + + 91 - -taxon_prefilter_metadmg_lca + +taxon_prefilter_metadmg_lca 52->91 - - + + 130 - -taxon_prefilter_metadmg_damage + +taxon_prefilter_metadmg_damage 52->130 - - + + 53 - -taxon_prefilter_shard_unicorn_refstats + +taxon_prefilter_shard_unicorn_refstats 53->52 - - + + 54 - -taxon_prefilter_shard_saturated_reads_remove + +taxon_prefilter_shard_saturated_reads_remove 54->53 - - + + 55->1 - - + + 55->54 - - + + - - -61 - -taxon_prefilter_shard_count_alns + + +57 + +taxon_prefilter_shard_count_alns - - -55->61 - - + + +55->57 + + 56 - -taxon_prefilter_shard_saturated_reads_filter + +taxon_prefilter_shard_saturated_reads_filter 56->50 - - + + 56->54 - - + + 63 - -taxon_prefilter_shard_saturated_reads_remove + +taxon_prefilter_shard_saturated_reads_remove 56->63 - - + + 65 - -taxon_prefilter_shard_saturated_reads_remove + +taxon_prefilter_shard_saturated_reads_remove 56->65 - - + + 56->128 - - - - - -57 - -taxon_prefilter_shard_count_alns + + 57->56 - - + + - - -58->1 - - + + +58 + +taxon_prefilter_shard_count_alns - - -58->57 - - + + +58->56 + + - + + +59->1 + + + + + +59->58 + + + + -58->63 - - +59->63 + + - - -59 - -taxon_prefilter_shard_count_alns + + +60 + +taxon_prefilter_shard_count_alns - - -59->56 - - + + +60->56 + + - - -60->1 - - + + +61->1 + + - - -60->59 - - + + +61->60 + + - + -60->65 - - - - - -61->56 - - +61->65 + + 62 - -taxon_prefilter_shard_unicorn_refstats + +taxon_prefilter_shard_unicorn_refstats 62->52 - - + + 63->62 - - + + 64 - -taxon_prefilter_shard_unicorn_refstats + +taxon_prefilter_shard_unicorn_refstats 64->52 - - + + 65->64 - - + + 66 - -prefilter_fastqc + +prefilter_fastqc 66->1 - - + + 67->66 - - - - - -97 - -taxon_shard_bowtie2 -n_shard: 1 -ref: mitoch -tot_shards: 1 - - - -67->97 - - + + 98 - -taxon_shard_bowtie2 -n_shard: 1 -ref: plastid -tot_shards: 1 + +taxon_shard_bowtie2 +n_shard: 1 +ref: plastid +tot_shards: 1 67->98 - - + + + + + +99 + +taxon_shard_bowtie2 +n_shard: 1 +ref: mitoch +tot_shards: 1 + + + +67->99 + + 68 - -prefilter_reads_merge + +prefilter_reads_merge 68->67 - - + + 69 - -prefilter_reads_taxonomy + +prefilter_reads_taxonomy 69->68 - - + + 70 - -taxon_prefilter_align_merge + +taxon_prefilter_align_merge 70->69 - - + + 85 - -taxon_prefilter_align_samtools_stats + +taxon_prefilter_align_samtools_stats 70->85 - - + + 89 - -taxon_prefilter_align_sort_taxon + +taxon_prefilter_align_sort_taxon 70->89 - - + + 93 - -taxon_prefilter_metadmg_lca + +taxon_prefilter_metadmg_lca 70->93 - - + + 131 - -taxon_prefilter_metadmg_damage + +taxon_prefilter_metadmg_damage 70->131 - - + + 71 - -taxon_prefilter_shard_unicorn_refstats + +taxon_prefilter_shard_unicorn_refstats 71->70 - - + + 72 - -taxon_prefilter_shard_saturated_reads_remove + +taxon_prefilter_shard_saturated_reads_remove 72->71 - - + + - + 73->1 - - + + 73->72 - - + + - - -79 - -taxon_prefilter_shard_count_alns + + +75 + +taxon_prefilter_shard_count_alns - - -73->79 - - + + +73->75 + + 74 - -taxon_prefilter_shard_saturated_reads_filter + +taxon_prefilter_shard_saturated_reads_filter 74->68 - - + + 74->72 - - + + 81 - -taxon_prefilter_shard_saturated_reads_remove + +taxon_prefilter_shard_saturated_reads_remove 74->81 - - + + 83 - -taxon_prefilter_shard_saturated_reads_remove + +taxon_prefilter_shard_saturated_reads_remove 74->83 - - + + 74->129 - - - - - -75 - -taxon_prefilter_shard_count_alns + + 75->74 - - + + - - -76->1 - - + + +76 + +taxon_prefilter_shard_count_alns - - -76->75 - - + + +76->74 + + + + + +77->1 + + - + + +77->76 + + + + -76->81 - - +77->81 + + - - -77 - -taxon_prefilter_shard_count_alns + + +78 + +taxon_prefilter_shard_count_alns - - -77->74 - - + + +78->74 + + - - -78->1 - - + + +79->1 + + - - -78->77 - - + + +79->78 + + - + -78->83 - - - - - -79->74 - - +79->83 + + 80 - -taxon_prefilter_shard_unicorn_refstats + +taxon_prefilter_shard_unicorn_refstats 80->70 - - + + 81->80 - - + + 82 - -taxon_prefilter_shard_unicorn_refstats + +taxon_prefilter_shard_unicorn_refstats 82->70 - - + + 83->82 - - + + 84->1 - - + + 85->1 - - + + 86 - -taxon_prefilter_align_unicorn_taxstats + +taxon_prefilter_align_unicorn_taxstats 86->1 - - + + 87->86 - - + + 88 - -taxon_prefilter_align_unicorn_taxstats + +taxon_prefilter_align_unicorn_taxstats 88->1 - - + + 89->88 - - + + 90 - -taxon_prefilter_metadmg_dfit + +taxon_prefilter_metadmg_dfit 90->1 - - + + 94 - -taxon_prefilter_metadmg_aggregate + +taxon_prefilter_metadmg_aggregate 90->94 - - + + 91->90 - - + + 91->94 - - + + 92 - -taxon_prefilter_metadmg_dfit + +taxon_prefilter_metadmg_dfit 92->1 - - + + 95 - -taxon_prefilter_metadmg_aggregate + +taxon_prefilter_metadmg_aggregate 92->95 - - + + 93->92 - - + + 93->95 - - + + 94->0 - - + + 94->1 - - + + 95->0 - - + + 95->1 - - + + 96->1 - - + + 103 - -taxon_shard_saturated_reads_remove + +taxon_shard_saturated_reads_remove 96->103 - - + + - - -106 - -taxon_shard_count_alns + + +105 + +taxon_shard_count_alns - - -96->106 - - + + +96->105 + + 97->1 - - + + - - -112 - -taxon_shard_saturated_reads_remove + + +106 + +taxon_shard_count_alns - - -97->112 - - + + +97->106 + + - - -115 - -taxon_shard_count_alns + + +108 + +taxon_shard_saturated_reads_remove - - -97->115 - - + + +97->108 + + 98->1 - - + + + + + +112 + +taxon_shard_saturated_reads_remove + + + +98->112 + + 114 - -taxon_shard_count_alns + +taxon_shard_count_alns 98->114 - - - - - -117 - -taxon_shard_saturated_reads_remove - - - -98->117 - - + + 99->1 - - + + - - -105 - -taxon_shard_count_alns + + +115 + +taxon_shard_count_alns - - -99->105 - - + + +99->115 + + - - -108 - -taxon_shard_saturated_reads_remove + + +117 + +taxon_shard_saturated_reads_remove - - -99->108 - - + + +99->117 + + 100 - -taxon_align_samtools_stats + +taxon_align_samtools_stats 100->1 - - + + 101 - -taxon_align_merge + +taxon_align_merge 101->100 - - + + 119 - -taxon_align_sort_taxon + +taxon_align_sort_taxon 101->119 - - + + 123 - -taxon_metadmg_lca + +taxon_metadmg_lca 101->123 - - + + 134 - -taxon_metadmg_damage + +taxon_metadmg_damage 101->134 - - + + 102 - -taxon_shard_unicorn_refstats + +taxon_shard_unicorn_refstats 102->101 - - + + 103->102 - - + + 104 - -taxon_shard_saturated_reads_filter + +taxon_shard_saturated_reads_filter 104->103 - - + + 104->108 - - + + 104->132 - - + + 105->104 - - + + 106->104 - - + + 107 - -taxon_shard_unicorn_refstats + +taxon_shard_unicorn_refstats 107->101 - - + + 108->107 - - + + 109 - -taxon_align_samtools_stats + +taxon_align_samtools_stats 109->1 - - + + 110 - -taxon_align_merge + +taxon_align_merge 110->109 - - + + 121 - -taxon_align_sort_taxon + +taxon_align_sort_taxon 110->121 - - + + 125 - -taxon_metadmg_lca + +taxon_metadmg_lca 110->125 - - + + 135 - -taxon_metadmg_damage + +taxon_metadmg_damage 110->135 - - + + 111 - -taxon_shard_unicorn_refstats + +taxon_shard_unicorn_refstats 111->110 - - + + 112->111 - - + + 113 - -taxon_shard_saturated_reads_filter + +taxon_shard_saturated_reads_filter 113->112 - - + + 113->117 - - + + 113->133 - - + + 114->113 - - + + 115->113 - - + + 116 - -taxon_shard_unicorn_refstats + +taxon_shard_unicorn_refstats 116->110 - - + + 117->116 - - + + 118 - -taxon_align_unicorn_taxstats + +taxon_align_unicorn_taxstats 118->1 - - + + 119->118 - - + + 120 - -taxon_align_unicorn_taxstats + +taxon_align_unicorn_taxstats 120->1 - - + + 121->120 - - + + 122 - -taxon_metadmg_dfit + +taxon_metadmg_dfit 122->1 - - + + 126 - -taxon_metadmg_aggregate + +taxon_metadmg_aggregate 122->126 - - + + 123->122 - - + + 123->126 - - + + 124 - -taxon_metadmg_dfit + +taxon_metadmg_dfit 124->1 - - + + 127 - -taxon_metadmg_aggregate + +taxon_metadmg_aggregate 124->127 - - + + 125->124 - - + + 125->127 - - + + 126->0 - - + + 126->1 - - + + 127->0 - - + + 127->1 - - + + 128->0 - - + + 129->0 - - + + 130->0 - - + + 131->0 - - + + 132->0 - - + + 133->0 - - + + 134->0 - - + + 135->0 - - + + diff --git a/examples/euk_prok_virus/filegraph.svg b/examples/euk_prok_virus/filegraph.svg index 4eb65e6..d3c7d75 100644 --- a/examples/euk_prok_virus/filegraph.svg +++ b/examples/euk_prok_virus/filegraph.svg @@ -40,7 +40,7 @@ output → -stats/reports/multiqc_taxon.upload.flag +temp/reports/multiqc_taxon.upload.log @@ -182,7 +182,7 @@ - + 2->1 @@ -238,7 +238,7 @@ - + 4->1 @@ -254,8 +254,8 @@ output → -stats/reads/fastqc/trim/{sample}_{library}_{lane}_{read_type_trim,collapsed|R2|R1|singleton|collapsedtrunc}.html -stats/reads/fastqc/trim/{sample}_{library}_{lane}_{read_type_trim,collapsed|R2|R1|singleton|collapsedtrunc}_fastqc.zip +stats/reads/fastqc/trim/{sample}_{library}_{lane}_{read_type_trim,collapsed|R2|singleton|R1|collapsedtrunc}.html +stats/reads/fastqc/trim/{sample}_{library}_{lane}_{read_type_trim,collapsed|R2|singleton|R1|collapsedtrunc}_fastqc.zip @@ -289,7 +289,7 @@ - + 5->1 @@ -312,7 +312,7 @@ - + 6->1 @@ -390,7 +390,7 @@ - + 8->1 @@ -402,7 +402,7 @@ - + 10->6 @@ -432,7 +432,7 @@ - + 11->6 @@ -455,7 +455,7 @@ - + 11->13 @@ -501,7 +501,7 @@ - + 11->40 @@ -547,7 +547,7 @@ - + 12->1 @@ -599,7 +599,7 @@ - + 14->13 @@ -703,7 +703,7 @@ ↪ input -<function <lambda> at 0x7f59c911b7e0> +<function <lambda> at 0x7f8f568e2c00> data/prok.acc2taxid.gz data/taxdump/names.dmp data/taxdump/nodes.dmp @@ -734,7 +734,7 @@ ↪ input -<function <lambda> at 0x7f59c911b600> +<function <lambda> at 0x7f8f568e2660> output → @@ -801,7 +801,7 @@ - + 19->1 @@ -865,7 +865,7 @@ - + 20->40 @@ -877,7 +877,7 @@ - + 22->1 @@ -931,7 +931,7 @@ - + 25->1 @@ -981,13 +981,13 @@ - + 27->1 - + 28->1 @@ -1054,7 +1054,7 @@ - + 29->1 @@ -1110,7 +1110,7 @@ ↪ input -<function <lambda> at 0x7f59c913b9c0> +<function <lambda> at 0x7f8f56943ba0> data/mitoch.acc2taxid.gz data/plastid.acc2taxid.gz data/taxdump/names.dmp @@ -1141,7 +1141,7 @@ ↪ input -<function <lambda> at 0x7f59c913ba60> +<function <lambda> at 0x7f8f56943880> output → @@ -1244,7 +1244,7 @@ - + 35->1 @@ -1274,7 +1274,7 @@ - + 37->1 @@ -1300,7 +1300,7 @@ - + 37->39 @@ -1312,43 +1312,43 @@ - + 38->39 - + 39->0 - + 39->1 - + 40->0 - + 41->0 - + 42->0 - + 43->0 diff --git a/examples/euk_prok_virus/rulegraph.svg b/examples/euk_prok_virus/rulegraph.svg index d3534ce..9cd6ec2 100644 --- a/examples/euk_prok_virus/rulegraph.svg +++ b/examples/euk_prok_virus/rulegraph.svg @@ -34,7 +34,7 @@ trim_fastqc_raw - + 2->1 @@ -64,7 +64,7 @@ - + 4->1 @@ -94,7 +94,7 @@ - + 5->1 @@ -112,7 +112,7 @@ - + 7->6 @@ -148,7 +148,7 @@ derep_nonpareil_plot - + 8->1 @@ -178,7 +178,7 @@ - + 11->6 @@ -190,7 +190,7 @@ prefilter_reads_extract - + 11->13 @@ -214,7 +214,7 @@ taxon_prefilter_shard_saturated_reads_extract - + 11->40 @@ -226,7 +226,7 @@ taxon_shard_saturated_reads_extract - + 11->42 @@ -238,7 +238,7 @@ prefilter_fastqc - + 12->1 @@ -268,7 +268,7 @@ prefilter_reads_merge - + 14->13 @@ -280,7 +280,7 @@ prefilter_reads_taxonomy - + 15->14 @@ -370,7 +370,7 @@ - + 19->1 @@ -400,7 +400,7 @@ taxon_prefilter_shard_saturated_reads_filter - + 20->14 @@ -412,7 +412,7 @@ - + 20->40 @@ -424,7 +424,7 @@ - + 22->1 @@ -436,7 +436,7 @@ taxon_prefilter_align_unicorn_taxstats - + 23->1 @@ -454,7 +454,7 @@ taxon_prefilter_metadmg_dfit - + 25->1 @@ -466,7 +466,7 @@ taxon_prefilter_metadmg_aggregate - + 25->27 @@ -478,25 +478,25 @@ - + 26->27 - + 27->0 - + 27->1 - + 28->1 @@ -508,7 +508,7 @@ taxon_shard_saturated_reads_remove - + 28->32 @@ -532,7 +532,7 @@ taxon_align_samtools_stats - + 29->1 @@ -610,13 +610,13 @@ taxon_shard_saturated_reads_filter - + 33->32 - + 33->42 @@ -634,7 +634,7 @@ taxon_align_unicorn_taxstats - + 35->1 @@ -652,7 +652,7 @@ taxon_metadmg_dfit - + 37->1 @@ -664,7 +664,7 @@ taxon_metadmg_aggregate - + 37->39 @@ -676,7 +676,7 @@ - + 38->39 @@ -688,31 +688,31 @@ - + 39->1 - + 40->0 - + 41->0 - + 42->0 - + 43->0