From a8dcd649176fee526a1a93b87cfcd5d8a4d88df2 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 20 Jul 2024 06:52:07 +0000 Subject: [PATCH] Update MQC so works on gitpod, try to re-add original getAllFilesFromDir (but not working - no md5swum?!) --- modules.json | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 10 +- modules/nf-core/multiqc/meta.yml | 13 + modules/nf-core/multiqc/tests/main.nf.test | 6 + .../nf-core/multiqc/tests/main.nf.test.snap | 18 +- tests/test.nf.test | 17 +- tests/test.nf.test.snap | 681 ++---------------- workflows/eager.nf | 4 +- 9 files changed, 100 insertions(+), 653 deletions(-) diff --git a/modules.json b/modules.json index 288e85c09..8f542cd8b 100644 --- a/modules.json +++ b/modules.json @@ -172,7 +172,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396", "installed_by": ["modules"] }, "picard/createsequencedictionary": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67e..2121492d6 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.23 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f9..459dfea5b 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' : + 'biocontainers/multiqc:1.23--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -26,6 +28,8 @@ process MULTIQC { def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ @@ -33,6 +37,8 @@ process MULTIQC { $config \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35e..382c08cbc 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -29,6 +29,19 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: type: file diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242ef..6aa27f4c9 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -17,6 +17,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +43,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +70,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd8029..45e95e5de 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } } \ No newline at end of file diff --git a/tests/test.nf.test b/tests/test.nf.test index 334cb5000..f128d329b 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -27,8 +27,8 @@ nextflow_pipeline { Exceptions (variable md5sums) */ - { assert snapshot( getAllFileNamesFromDir("$outputDir/damage_estimation/", '.txt') ).match("damage_estimation_txt") }, - { assert snapshot( getAllFileNamesFromDir("$outputDir/damage_estimation/", '.json') ).match("damage_estimation_json") }, + { assert snapshot( getAllFilesFromDir("$outputDir/damage_estimation/", '.txt') ).match("damage_estimation_txt") }, + { assert snapshot( getAllFilesFromDir("$outputDir/damage_estimation/", '.json') ).match("damage_estimation_json") }, { assert snapshot( getAllFileNamesFromDir("$outputDir/damage_estimation/", '.svg') ).match("damage_estimation_svg") }, { assert snapshot( getAllFileNamesFromDir("$outputDir/damage_estimation/", '.pdf') ).match("damage_estimation_pdf") }, { assert snapshot( checkAllFilesNamesFromDirForString("$outputDir/damage_estimation/", '.log', 'FINISHED SUCCESSFULLY') ).match("damage_estimation_log") }, @@ -46,6 +46,17 @@ nextflow_pipeline { } // Recursively list all files in a directory and its subdirectories matching a given suffix +def getAllFilesFromDir(dir, suffix) { + def output = [] + new File(dir).eachFileRecurse() { + if (it.name.toString().matches(".*\\.${suffix}")) { + output.add(file(it)) + } + } + return output +} + +// Recursively list all files names in a directory and its subdirectories matching a given suffix def getAllFileNamesFromDir(dir, suffix) { def output = [] new File(dir).eachFileRecurse() { @@ -70,7 +81,7 @@ def checkAllFilesNamesFromDirForString(dir, suffix, string) { //def getAllFilesFromDir(dir, suffix) { // def output = [] // new File(dir).eachFileRecurse() { -// if (it.name.toString().matches(".*\\.(${suffix.join('|')})")) { +// if (it.name.toString().matches(".*\\.${suffix}")) { // output.add(it) // } // } diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 8945bd44c..eee2b61eb 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -1,303 +1,35 @@ { - "processing_fastp": { - "content": [ - [ - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.html:md5,1f497b8535aa0e4281988cd14d04e4c1", - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.json:md5,f9ac29dc38bd5e51beb9ea5a8a8e22f3", - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.log:md5,e7e2e16afe04f4d70e5fad458079c64b", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.html:md5,341ecbfbb2103d8e9ce20113ffea7736", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.json:md5,582794e200f2ddf0aad317ab42f88e79", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.log:md5,cc245eaecedc85ef9e4d0f0e6b1f1c45" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-28T13:32:44.409297996" - }, "damage_estimation_txt": { "content": [ [ - "3pGtoA_freq.txt", - "editDistance.txt", - "DNA_composition_sample.txt", - "lgdistribution.txt", - "5p_freq_misincorporations.txt", - "misincorporation.txt", - "DNA_comp_genome.txt", - "5pCtoT_freq.txt", - "3p_freq_misincorporations.txt", - "3pGtoA_freq.txt", - "editDistance.txt", - "DNA_composition_sample.txt", - "lgdistribution.txt", - "5p_freq_misincorporations.txt", - "misincorporation.txt", - "DNA_comp_genome.txt", - "5pCtoT_freq.txt", - "3p_freq_misincorporations.txt", - "3pGtoA_freq.txt", - "editDistance.txt", - "DNA_composition_sample.txt", - "lgdistribution.txt", - "5p_freq_misincorporations.txt", - "misincorporation.txt", - "DNA_comp_genome.txt", - "5pCtoT_freq.txt", - "3p_freq_misincorporations.txt" + ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T16:21:00.738565595" + "timestamp": "2024-07-20T06:30:48.92614635" }, "damage_estimation_pdf": { "content": [ [ - "edit_distance.pdf", - "Length_plot.pdf", "DamagePlot.pdf", - "edit_distance.pdf", "Length_plot.pdf", + "edit_distance.pdf", "DamagePlot.pdf", + "Length_plot.pdf", "edit_distance.pdf", + "DamagePlot.pdf", "Length_plot.pdf", - "DamagePlot.pdf" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-19T16:14:44.22399099" - }, - "mapstats": { - "content": [ - [ - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_breadth.bed:md5,45b641735c8e2b4be10766a5c246068d", - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_depth.bed:md5,2b6ffd36b2fb3b8b2b52b928d7a63158", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_breadth.bed:md5,5286794122bb3c67d49cc858d40f0c31", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_depth.bed:md5,5065bd5c0001f20bf4f03d62297cf4ca", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_breadth.bed:md5,16b5f8952d87e236a63e681293691832", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_depth.bed:md5,1b4f117a16c712b7c67809d7e4ec279f", - "versions.yml:md5,f6c22504bd960903cef378d15aa1cf99" - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,a3ccef0b8d19d69457b817898a2a5604", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,58df3f7e6ba65086daa94e49fe6b60f3", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,f771d9d15a744ea8a7031d36551ec7b3" - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause.c_curve.txt:md5,ba8059ca2396fb898593c1e66e56a7bc", - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause.command.log:md5,d41d8cd98f00b204e9800998ecf8427e", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause.c_curve.txt:md5,817f35dc7ce2983a7d0f558debd6e94b", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause.command.log:md5,d41d8cd98f00b204e9800998ecf8427e", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause.c_curve.txt:md5,1384a88b531ab872c0069e71fccbe97a", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause.command.log:md5,d41d8cd98f00b204e9800998ecf8427e", - "versions.yml:md5,04edb6451354c81b20ffba3102b625b8" - ], - [ - [ - [ - [ - [ - [ - "agogo.css:md5,bd757b1a7ce6fdc0288ba148680f4583", - "ajax-loader.gif:md5,ae6667053ad118020b8e68ccf307b519", - "basic.css:md5,25b2823342c0604924a2870eeb4e7e94", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "doctools.js:md5,5ff571aa60e63f69c1890283e240ff8d", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "jquery.js:md5,10092eee563dec2dca82b77d2cf5a1ae", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "pygments.css:md5,d625a0adb949f181bd0d3f1432b0fa7f", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "report.css:md5,7a5f09eaf7c176f966f4e8854168b812", - "searchtools.js:md5,d550841adeedc8ed47c40ee607620937", - "underscore.js:md5,db5ba047a66617d4cd3e8c5099cc51db", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "websupport.js:md5,9e61e1e8a7433c56bd7e5a615affcf85" - ], - "genome_results.txt:md5,77e34a3588c1743562d89580054a0307", - [ - "genome_coverage_0to50_histogram.png:md5,80aa3c94722e4c938393a45b7015a813", - "genome_coverage_across_reference.png:md5,64b7b05ec75f24d60cb779d234fc2399", - "genome_coverage_histogram.png:md5,ef7314fa488b67773f9174cfd96a7b64", - "genome_coverage_quotes.png:md5,7e83e24f741f74978d5c1ed479d86eb2", - "genome_gc_content_per_window.png:md5,e0e20c8a65b6d41c88a6a2ef44a9ec1a", - "genome_homopolymer_indels.png:md5,e2cdb644cfca349cc7a7151175d32f0d", - "genome_mapping_quality_across_reference.png:md5,7108d78085bef09350214151e3429b89", - "genome_mapping_quality_histogram.png:md5,a9f0ca725de66c600d127baeff3d63ea", - "genome_reads_content_per_read_position.png:md5,650b98e61e3bc39351effe0a79c21876", - "genome_uniq_read_starts_histogram.png:md5,d1e870f849ba228e52d5be513eb86c8a" - ], - "qualimapReport.html:md5,4d422382371f26a3b25479356dc1413c", - [ - "coverage_across_reference.txt:md5,b724388bf0301fb73cc95adcd99f3e9f", - "coverage_histogram.txt:md5,402146079b9e04bc1acc5f02e7b61d7c", - "duplication_rate_histogram.txt:md5,e6f1a6e48ba04b2aa69a09b56e10962b", - "genome_fraction_coverage.txt:md5,058852542e5052d456c3e41b2ad7fe68", - "homopolymer_indels.txt:md5,2cc3cb5d9105a4d5feca2b3dbe32494e", - "mapped_reads_gc-content_distribution.txt:md5,3262dd7abf0325ccc7935277ecff9458", - "mapped_reads_nucleotide_content.txt:md5,714ea0b92f3d0919bda34ee521035b47", - "mapping_quality_across_reference.txt:md5,bde42f64a3d9d8611a76a2402fa29fb2", - "mapping_quality_histogram.txt:md5,3943155d987a6d966950b4b77666cd4e" - ] - ], - "versions.yml:md5,1f32280851a9253616996ce3b72d0c04" - ] - ], - [ - [ - [ - [ - "agogo.css:md5,bd757b1a7ce6fdc0288ba148680f4583", - "ajax-loader.gif:md5,ae6667053ad118020b8e68ccf307b519", - "basic.css:md5,25b2823342c0604924a2870eeb4e7e94", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "doctools.js:md5,5ff571aa60e63f69c1890283e240ff8d", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "jquery.js:md5,10092eee563dec2dca82b77d2cf5a1ae", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "pygments.css:md5,d625a0adb949f181bd0d3f1432b0fa7f", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "report.css:md5,7a5f09eaf7c176f966f4e8854168b812", - "searchtools.js:md5,d550841adeedc8ed47c40ee607620937", - "underscore.js:md5,db5ba047a66617d4cd3e8c5099cc51db", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "websupport.js:md5,9e61e1e8a7433c56bd7e5a615affcf85" - ], - "genome_results.txt:md5,10318c6586c06f3d7d3a68cb0b53ed26", - [ - "genome_coverage_0to50_histogram.png:md5,405e3b012c5092a33e099042c7a479f8", - "genome_coverage_across_reference.png:md5,96f145a33a8c56cdaebb7f0197c476e4", - "genome_coverage_histogram.png:md5,53ad483690ce3db0286c493421b165f5", - "genome_coverage_quotes.png:md5,dea5046f36d0963ee25ca1ac51154382", - "genome_gc_content_per_window.png:md5,8206f9e95c9889911668f38a154faa52", - "genome_homopolymer_indels.png:md5,66811ef0c7fe5e32392e8dfced3c68f1", - "genome_mapping_quality_across_reference.png:md5,61a09c6116481dc68b408683d8d5d09c", - "genome_mapping_quality_histogram.png:md5,50c3e22a2d17c314ad30b06ff7993396", - "genome_reads_clipping_profile.png:md5,386954c65ba40aee3129aa3fd840445d", - "genome_reads_content_per_read_position.png:md5,587bd7978b3e18a65099f06c119c3f04", - "genome_uniq_read_starts_histogram.png:md5,4f7305df090a4ad3bc87342740d414ef" - ], - "qualimapReport.html:md5,19c6ee72e4df282ed3b40e0a81dcbcf8", - [ - "coverage_across_reference.txt:md5,3be6bd7fef9e81d56792b58e902949ed", - "coverage_histogram.txt:md5,8aaee99c160b7b5e030ee6fc891d9837", - "duplication_rate_histogram.txt:md5,ffd92c4701b07a4f3b6a580928770fe4", - "genome_fraction_coverage.txt:md5,f2e4bc958f9df721a6adccbc69de9706", - "homopolymer_indels.txt:md5,e6beb36c6aab5de9cb6d9e2357f82995", - "mapped_reads_clipping_profile.txt:md5,f3ee469d515a49d50ac4e438ddfc8b57", - "mapped_reads_gc-content_distribution.txt:md5,818ed0f391e3d08fee4f102721127976", - "mapped_reads_nucleotide_content.txt:md5,058c7dc070f76bc2c1913595070f9066", - "mapping_quality_across_reference.txt:md5,fb2c0f2f4c95c698ab67520cb3f2db5a", - "mapping_quality_histogram.txt:md5,4c5a2755f3eec182031390f7bb0d4d0f" - ] - ], - "versions.yml:md5,1f32280851a9253616996ce3b72d0c04" - ] - ] - ] - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-28T13:32:44.2518606" - }, - "preprocessing": { - "content": [ - [ - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.html:md5,9d9776be3f01ac03bb27f5c9c8a3e687", - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.json:md5,f9ac29dc38bd5e51beb9ea5a8a8e22f3", - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.log:md5,e7e2e16afe04f4d70e5fad458079c64b", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.html:md5,e623e6dfc2ce121ad19e9f49bfd5c50a", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.json:md5,582794e200f2ddf0aad317ab42f88e79", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.log:md5,cc245eaecedc85ef9e4d0f0e6b1f1c45", - [ - "JK2782_JK2782_TGGCCGATCAACGA_L1_fastqc.html:md5,1fa3536dbdfde4b5272a185a61ee4a21", - "JK2782_JK2782_TGGCCGATCAACGA_L1_fastqc.zip:md5,f7e8782c04288a48db09ff28c48c9646", - "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,817b8430741eeb8c30475c51cd4eaac9", - "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip:md5,8893254a98c1189fa6ebf5ee4f5a1a5f", - "versions.yml:md5,42fbb757df8018b4595df690155d41d2" - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html:md5,57632a1d575aa5874a82afdfa34efd07", - "JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.zip:md5,2fba3491d0f4f00387f3e2fa2eb8ae4f", - "JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html:md5,1259416f24996b643197febdc878172a", - "JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.zip:md5,d74aae16484c87c43df704c5688bb605", - "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,8d4b1e3cf12c25d899538c21c9227b5e", - "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip:md5,e558f1b3f95c9dd2f2b4a67486cce4f0", - "versions.yml:md5,b4672add0ce3c990afa1a2bc9f6a7c87" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-28T11:28:50.209617559" - }, - "damage_estimation": { - "content": [ - [ - "3pGtoA_freq.txt:md5,59aa1691a1c420dffeff4edc4a9cb0dd", - "editDistance.txt:md5,5feeaa4b7018320fd9937e271299375c", - "DNA_composition_sample.txt:md5,0a4d26c613bbc4541eb51ec1344d6ef4", - "lgdistribution.txt:md5,3728eba42dd0b577a8566c103c342eb4", - "5p_freq_misincorporations.txt:md5,fc0939e3e176deef644c0bd24cb0d141", - "misincorporation.txt:md5,a2d9fed1148fe02e372f0905c7e15b40", - "DNA_comp_genome.txt:md5,76762da07599aff410c2ec531cd19720", - "5pCtoT_freq.txt:md5,51511bb6d9278afeb35099ab8b117119", - "3p_freq_misincorporations.txt:md5,15f64d35fc97bab2fed172fec292c3c9", - "3pGtoA_freq.txt:md5,c32ef382b55fed96816df63993c520eb", - "editDistance.txt:md5,7c00cd7cc4bd87c2da4debaa2704a66a", - "DNA_composition_sample.txt:md5,1336769b56151d9de542610c4a8ef662", - "lgdistribution.txt:md5,3c176293ea8e58d1d56a95e693727f7a", - "5p_freq_misincorporations.txt:md5,af2192b8a97699519d060baa3c8982fe", - "misincorporation.txt:md5,e25101ff61a0a3c377f8bc0252ee4451", - "DNA_comp_genome.txt:md5,0f27b55f4a7c2731f35761be4feddbfa", - "5pCtoT_freq.txt:md5,d6e1401fb49387f83d842977ee47a9d2", - "3p_freq_misincorporations.txt:md5,2d4d9e2906c2238d27fa7e441bba2b33", - "3pGtoA_freq.txt:md5,24ae86cb4dd4e558412344a98d582bae", - "editDistance.txt:md5,059c352bf858c5ddb27e88253654e353", - "DNA_composition_sample.txt:md5,dd78c33e4d9367759e82c31247685a3b", - "lgdistribution.txt:md5,5e8760bf271b743aa3c7c96414fb9991", - "5p_freq_misincorporations.txt:md5,8ecb71fca75a2f86cf44eb0cf4bfd269", - "misincorporation.txt:md5,983d8fab464d67481b222aff57b06587", - "DNA_comp_genome.txt:md5,b78d2826f0e1be4990120105c83d0b06", - "5pCtoT_freq.txt:md5,5a04f777d38930e205213298e70e09f1", - "3p_freq_misincorporations.txt:md5,fe312a520a01f198bf248f396b179aff" + "edit_distance.pdf" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T11:30:08.690300717" + "timestamp": "2024-07-20T06:30:49.433055327" }, "samtools": { "content": [ @@ -311,23 +43,6 @@ }, "timestamp": "2024-06-28T13:08:37.202608535" }, - "final_bams": { - "content": [ - [ - "JK2782_Mammoth_MT_Krause.bam:md5,c83509e57eba69bcb5413ce03ed6618b", - "JK2782_Mammoth_MT_Krause.bam.bai:md5,cdad2a0d2a39bdbd689d4b0ffbac8383", - "JK2782_Mammoth_MT_Krause.flagstat:md5,04ff612d7bb381cca5bda876b7ed7d13", - "JK2802_Mammoth_MT_Krause.bam:md5,475ffdc52e1297e273e6a2a2d5366218", - "JK2802_Mammoth_MT_Krause.bam.bai:md5,b47aef8c46ca45c22384f43ef96ee1f8", - "JK2802_Mammoth_MT_Krause.flagstat:md5,fb4d234136f242c20db27979caa604cf" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-28T13:32:44.111408553" - }, "bam_filtering": { "content": [ [ @@ -348,292 +63,6 @@ }, "timestamp": "2024-06-28T11:25:56.604142252" }, - "test_profile": { - "content": [ - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_filtered.bam.bai:md5,d1823ee5a37ad32007d0923731127935", - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_filtered.flagstat:md5,39fd430cc77fc71f71d75a221c1b7880", - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_lengthonly.filtered.bam.bai:md5,159e97ddc9270c8d941f42f5553cf4fe", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_filtered.bam.bai:md5,3829853588ac224ac094d93054c7fbef", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_filtered.flagstat:md5,a9fbd8c9a6f8bb02b191f4140f91d04a", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_lengthonly.filtered.bam.bai:md5,cea7aec832f94e0221bb7da743f3e16c", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_filtered.bam.bai:md5,8f0a7ad0e353b6714701a6c5ae54d3f1", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_filtered.flagstat:md5,f6c739b729c06e17ca205c64478ad823", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_lengthonly.filtered.bam.bai:md5,43a0d7aaeb7c8dae073c829504a4278f" - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_8_Mammoth_MT_Krause.flagstat:md5,9a10991f5670a52975a622a8b056e2bc" - ], - [ - [ - [ - "3pGtoA_freq.txt:md5,c32ef382b55fed96816df63993c520eb", - "3p_freq_misincorporations.txt:md5,2d4d9e2906c2238d27fa7e441bba2b33", - "5pCtoT_freq.txt:md5,d6e1401fb49387f83d842977ee47a9d2", - "5p_freq_misincorporations.txt:md5,af2192b8a97699519d060baa3c8982fe", - "DNA_comp_genome.txt:md5,0f27b55f4a7c2731f35761be4feddbfa", - "DNA_composition_sample.txt:md5,1336769b56151d9de542610c4a8ef662", - "DamagePlot.pdf:md5,5b3256627f9f626230da579db61e5c49", - "DamagePlot_five_prime.svg:md5,7210e8b3200886b87634a49ae0f9a8ac", - "DamagePlot_three_prime.svg:md5,597a75d31ef402299f12c2b2fa58c104", - "DamageProfiler.log:md5,536a0a3084fb69ba4ae0f7d8358645c3", - "Length_plot.pdf:md5,4e81f7470ea0fb0bc930e1a4322e99d3", - "Length_plot_combined_data.svg:md5,277139e458c49f1d212dbbe809273212", - "Length_plot_forward_reverse_separated.svg:md5,4253d607d3f4cbbafdc43464d4175beb", - "dmgprof.json:md5,e829fb37f3e12842a6139e1d4cfe19dc", - "editDistance.txt:md5,7c00cd7cc4bd87c2da4debaa2704a66a", - "edit_distance.pdf:md5,89a3d200f8726b09200a822d01465122", - "edit_distance.svg:md5,7e6dd9adfa4ad06467d0a9bf2c2267b4", - "lgdistribution.txt:md5,3c176293ea8e58d1d56a95e693727f7a", - "misincorporation.txt:md5,e25101ff61a0a3c377f8bc0252ee4451" - ], - [ - "3pGtoA_freq.txt:md5,59aa1691a1c420dffeff4edc4a9cb0dd", - "3p_freq_misincorporations.txt:md5,15f64d35fc97bab2fed172fec292c3c9", - "5pCtoT_freq.txt:md5,51511bb6d9278afeb35099ab8b117119", - "5p_freq_misincorporations.txt:md5,fc0939e3e176deef644c0bd24cb0d141", - "DNA_comp_genome.txt:md5,76762da07599aff410c2ec531cd19720", - "DNA_composition_sample.txt:md5,0a4d26c613bbc4541eb51ec1344d6ef4", - "DamagePlot.pdf:md5,2a46a3a924f8dc437b9721e286bcec4e", - "DamagePlot_five_prime.svg:md5,6f22636e53077bf58ad580aaff3c46b5", - "DamagePlot_three_prime.svg:md5,e637fe0d0714353c4a9fb53850c0488a", - "DamageProfiler.log:md5,67737d39ccb560360a9fdc8bd50870ad", - "Length_plot.pdf:md5,f48781427f21141bb45daafb320b11cc", - "Length_plot_combined_data.svg:md5,78b1e126e716baeb56789487baec1029", - "Length_plot_forward_reverse_separated.svg:md5,f8fe7e8b91acb747fa24dd612bbcdb10", - "dmgprof.json:md5,49a1a9b445abf48904ead652a16fb7e4", - "editDistance.txt:md5,5feeaa4b7018320fd9937e271299375c", - "edit_distance.pdf:md5,b8e7838941b6e98f5417148ce01e87ee", - "edit_distance.svg:md5,ce03bb5b0a22472b5ff2d4d8126db307", - "lgdistribution.txt:md5,3728eba42dd0b577a8566c103c342eb4", - "misincorporation.txt:md5,a2d9fed1148fe02e372f0905c7e15b40" - ], - [ - "3pGtoA_freq.txt:md5,24ae86cb4dd4e558412344a98d582bae", - "3p_freq_misincorporations.txt:md5,fe312a520a01f198bf248f396b179aff", - "5pCtoT_freq.txt:md5,5a04f777d38930e205213298e70e09f1", - "5p_freq_misincorporations.txt:md5,8ecb71fca75a2f86cf44eb0cf4bfd269", - "DNA_comp_genome.txt:md5,b78d2826f0e1be4990120105c83d0b06", - "DNA_composition_sample.txt:md5,dd78c33e4d9367759e82c31247685a3b", - "DamagePlot.pdf:md5,c34cec114dae1a97b78301e3b08f9c62", - "DamagePlot_five_prime.svg:md5,6d3ca494a8fce37fea8d4c7757df45e6", - "DamagePlot_three_prime.svg:md5,5a1ac5f56161f64f3f8f46a7ffcaf476", - "DamageProfiler.log:md5,d9060eb0059ac4fe6b18c7924da6627d", - "Length_plot.pdf:md5,8f0624914b21a859874751d70c6f82d5", - "Length_plot_combined_data.svg:md5,c09ccfdc611c76eb94028ae495d9f607", - "Length_plot_forward_reverse_separated.svg:md5,d24f085a7aa3cfd1243d10fd2105e01b", - "dmgprof.json:md5,98c584c20659b11692cbd1e280deeb97", - "editDistance.txt:md5,059c352bf858c5ddb27e88253654e353", - "edit_distance.pdf:md5,aedab720d1203511e972c8b401828562", - "edit_distance.svg:md5,e5a5fade20a089058fb2ba242d31207e", - "lgdistribution.txt:md5,5e8760bf271b743aa3c7c96414fb9991", - "misincorporation.txt:md5,983d8fab464d67481b222aff57b06587" - ], - "versions.yml:md5,2814e619e5090776204ba0c2edfa07c2" - ] - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.bam:md5,cafd8aec87c34a34a599aaf881bac4c2", - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.bam.bai:md5,196d7c4df7b32afc5209fdf7fff96a37", - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_dedupped.flagstat:md5,715d840d3bab5a05934825cd9b799ef3", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.bam:md5,5d76afc0e40def51f3078613b1f1940f", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.bam.bai:md5,9efc80f161fda84978104195171fe4d3", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_dedupped.flagstat:md5,dde5f59b006afdae2ff5fab85bc8ea92", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.bam:md5,8f105b750d30fe800171fd1b6253796a", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.bam.bai:md5,51dc155d22f4996a7fe3abb8094767a0", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_dedupped.flagstat:md5,fb4d234136f242c20db27979caa604cf" - ], - [ - "JK2782_Mammoth_MT_Krause.bam:md5,fa3e975cd3cb8fe793c7005997a529fe", - "JK2782_Mammoth_MT_Krause.bam.bai:md5,413f61b8135183ae5b362d446d296f38", - "JK2782_Mammoth_MT_Krause.flagstat:md5,04ff612d7bb381cca5bda876b7ed7d13", - "JK2802_Mammoth_MT_Krause.bam:md5,475ffdc52e1297e273e6a2a2d5366218", - "JK2802_Mammoth_MT_Krause.bam.bai:md5,b47aef8c46ca45c22384f43ef96ee1f8", - "JK2802_Mammoth_MT_Krause.flagstat:md5,fb4d234136f242c20db27979caa604cf" - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause.flagstat:md5,98a2f8bb2aa9678e4cf9578ee9ab3b0e", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam:md5,8782b5bda9a8dfece65c519ccee282a8", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam.bai:md5,ff81f602fb30d6b2e1e5ce86d53a0fc6", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause.flagstat:md5,cb86b29c65c8c123a8863330316c6400", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam:md5,f0bd835b6b75e71a911d7c2d8ae1e417", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam.bai:md5,bd4b258295870212b018eee0ba9dd22d" - ], - [ - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_breadth.bed:md5,45b641735c8e2b4be10766a5c246068d", - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_depth.bed:md5,2b6ffd36b2fb3b8b2b52b928d7a63158", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_breadth.bed:md5,5286794122bb3c67d49cc858d40f0c31", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_depth.bed:md5,5065bd5c0001f20bf4f03d62297cf4ca", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_breadth.bed:md5,16b5f8952d87e236a63e681293691832", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_depth.bed:md5,1b4f117a16c712b7c67809d7e4ec279f", - "versions.yml:md5,f6c22504bd960903cef378d15aa1cf99" - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,a3ccef0b8d19d69457b817898a2a5604", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,58df3f7e6ba65086daa94e49fe6b60f3", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,f771d9d15a744ea8a7031d36551ec7b3" - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause.c_curve.txt:md5,ba8059ca2396fb898593c1e66e56a7bc", - "JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause.command.log:md5,d41d8cd98f00b204e9800998ecf8427e", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause.c_curve.txt:md5,817f35dc7ce2983a7d0f558debd6e94b", - "JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause.command.log:md5,d41d8cd98f00b204e9800998ecf8427e", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause.c_curve.txt:md5,1384a88b531ab872c0069e71fccbe97a", - "JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause.command.log:md5,d41d8cd98f00b204e9800998ecf8427e", - "versions.yml:md5,04edb6451354c81b20ffba3102b625b8" - ], - [ - [ - [ - [ - [ - [ - "agogo.css:md5,bd757b1a7ce6fdc0288ba148680f4583", - "ajax-loader.gif:md5,ae6667053ad118020b8e68ccf307b519", - "basic.css:md5,25b2823342c0604924a2870eeb4e7e94", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "doctools.js:md5,5ff571aa60e63f69c1890283e240ff8d", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "jquery.js:md5,10092eee563dec2dca82b77d2cf5a1ae", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "pygments.css:md5,d625a0adb949f181bd0d3f1432b0fa7f", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "report.css:md5,7a5f09eaf7c176f966f4e8854168b812", - "searchtools.js:md5,d550841adeedc8ed47c40ee607620937", - "underscore.js:md5,db5ba047a66617d4cd3e8c5099cc51db", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "websupport.js:md5,9e61e1e8a7433c56bd7e5a615affcf85" - ], - "genome_results.txt:md5,bed8dd40a1960be1e27f078ebc275c72", - [ - "genome_coverage_0to50_histogram.png:md5,eb29e0180058c837d275b0253fe50b8d", - "genome_coverage_across_reference.png:md5,e5ea8086fd0d512eef4ae5bb6014c50d", - "genome_coverage_histogram.png:md5,b8cf92a57b487da85b391a6844821e65", - "genome_coverage_quotes.png:md5,3336998ed9ec412cabb783858264c55f", - "genome_gc_content_per_window.png:md5,afa61450a1945d3abd7b6f5eba8e11b4", - "genome_homopolymer_indels.png:md5,cc446ea163990a3881ea3f53216beaec", - "genome_mapping_quality_across_reference.png:md5,0e32ab0698e64e2136a5ad9d692839f7", - "genome_mapping_quality_histogram.png:md5,cd3610da594d50dcae9ffb741301951e", - "genome_reads_content_per_read_position.png:md5,a4a6fd6472da7e2f3f5fc3de382cb26a", - "genome_uniq_read_starts_histogram.png:md5,e36ced7d2c5fe81b57c3a438cfa7d2d0" - ], - "qualimapReport.html:md5,69924d9310a4cebe5a2f3491bde5d359", - [ - "coverage_across_reference.txt:md5,a3b137574b656048055259e3701dfa66", - "coverage_histogram.txt:md5,ef11ed244dea633816635cef4f6ccda2", - "duplication_rate_histogram.txt:md5,8de6fc70137f8be2f33ecc5b7e2f2fcb", - "genome_fraction_coverage.txt:md5,c4a5b85386d67af270ca1f6bd1f6be91", - "homopolymer_indels.txt:md5,28817a010a023836fcf6aac4e1e3976f", - "mapped_reads_gc-content_distribution.txt:md5,bf2a85175315e6cf13e2bd861f213977", - "mapped_reads_nucleotide_content.txt:md5,bc7b633508a2b831ecb2d7522824fe25", - "mapping_quality_across_reference.txt:md5,88854b58e0eb73b589be5da543b0189f", - "mapping_quality_histogram.txt:md5,78ac23aa0a0184e4a06144e7a488828d" - ] - ], - "versions.yml:md5,1f32280851a9253616996ce3b72d0c04" - ] - ], - [ - [ - [ - [ - "agogo.css:md5,bd757b1a7ce6fdc0288ba148680f4583", - "ajax-loader.gif:md5,ae6667053ad118020b8e68ccf307b519", - "basic.css:md5,25b2823342c0604924a2870eeb4e7e94", - "bgfooter.png:md5,ed01bb040346e4623cc87de331ddb4e1", - "bgtop.png:md5,626a50532dc6e5adbdd968746ef318e8", - "comment-bright.png:md5,0c850bb4920b581bf5e5dba5fa493a64", - "comment-close.png:md5,2635dda49c823e8122d4d11ed385f33d", - "comment.png:md5,882e40f3d6a16c6ed35659b105251525", - "doctools.js:md5,5ff571aa60e63f69c1890283e240ff8d", - "down-pressed.png:md5,ebe8979581eda700fb234a73c661a4b9", - "down.png:md5,f6f3c819cc7ca27d7fd3347e5e7ffe0f", - "file.png:md5,6587e59c55e626744eb6fc11129d99a7", - "jquery.js:md5,10092eee563dec2dca82b77d2cf5a1ae", - "minus.png:md5,8d572395aa95c89584a09813ada4dfa1", - "plus.png:md5,0125e6faa04e2cf0141a2d599d3bb220", - "pygments.css:md5,d625a0adb949f181bd0d3f1432b0fa7f", - "qualimap_logo_small.png:md5,7526f145a97be4682fd59e27dda4f71b", - "report.css:md5,7a5f09eaf7c176f966f4e8854168b812", - "searchtools.js:md5,d550841adeedc8ed47c40ee607620937", - "underscore.js:md5,db5ba047a66617d4cd3e8c5099cc51db", - "up-pressed.png:md5,8ea9bd109342f87fee97943b479c6f7e", - "up.png:md5,ecc373278454cc8ecc12d6ca69e55b36", - "websupport.js:md5,9e61e1e8a7433c56bd7e5a615affcf85" - ], - "genome_results.txt:md5,10318c6586c06f3d7d3a68cb0b53ed26", - [ - "genome_coverage_0to50_histogram.png:md5,405e3b012c5092a33e099042c7a479f8", - "genome_coverage_across_reference.png:md5,96f145a33a8c56cdaebb7f0197c476e4", - "genome_coverage_histogram.png:md5,53ad483690ce3db0286c493421b165f5", - "genome_coverage_quotes.png:md5,dea5046f36d0963ee25ca1ac51154382", - "genome_gc_content_per_window.png:md5,8206f9e95c9889911668f38a154faa52", - "genome_homopolymer_indels.png:md5,66811ef0c7fe5e32392e8dfced3c68f1", - "genome_mapping_quality_across_reference.png:md5,61a09c6116481dc68b408683d8d5d09c", - "genome_mapping_quality_histogram.png:md5,50c3e22a2d17c314ad30b06ff7993396", - "genome_reads_clipping_profile.png:md5,386954c65ba40aee3129aa3fd840445d", - "genome_reads_content_per_read_position.png:md5,587bd7978b3e18a65099f06c119c3f04", - "genome_uniq_read_starts_histogram.png:md5,4f7305df090a4ad3bc87342740d414ef" - ], - "qualimapReport.html:md5,a26aec748f50f5fa474dbca446ccb950", - [ - "coverage_across_reference.txt:md5,3be6bd7fef9e81d56792b58e902949ed", - "coverage_histogram.txt:md5,8aaee99c160b7b5e030ee6fc891d9837", - "duplication_rate_histogram.txt:md5,ffd92c4701b07a4f3b6a580928770fe4", - "genome_fraction_coverage.txt:md5,f2e4bc958f9df721a6adccbc69de9706", - "homopolymer_indels.txt:md5,e6beb36c6aab5de9cb6d9e2357f82995", - "mapped_reads_clipping_profile.txt:md5,f3ee469d515a49d50ac4e438ddfc8b57", - "mapped_reads_gc-content_distribution.txt:md5,818ed0f391e3d08fee4f102721127976", - "mapped_reads_nucleotide_content.txt:md5,058c7dc070f76bc2c1913595070f9066", - "mapping_quality_across_reference.txt:md5,fb2c0f2f4c95c698ab67520cb3f2db5a", - "mapping_quality_histogram.txt:md5,4c5a2755f3eec182031390f7bb0d4d0f" - ] - ], - "versions.yml:md5,1f32280851a9253616996ce3b72d0c04" - ] - ] - ] - ] - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.html", - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.json", - "JK2782_JK2782_TGGCCGATCAACGA_L1.fastp.log", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.html", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.json", - "JK2802_JK2802_AGAATAACCTACCA_L2.fastp.log", - "fastqc_processed/JK2782_JK2782_TGGCCGATCAACGA_L1_fastqc.html", - "fastqc_processed/JK2782_JK2782_TGGCCGATCAACGA_L1_fastqc.zip", - "fastqc_processed/JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html", - "fastqc_processed/JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip", - "fastqc_processed/versions.yml", - "fastqc_raw/JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html", - "fastqc_raw/JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.zip", - "fastqc_raw/JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html", - "fastqc_raw/JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.zip", - "fastqc_raw/JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html", - "fastqc_raw/JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip", - "fastqc_raw/versions.yml" - ], - [ - "JK2782_JK2782_TGGCCGATCAACGA_BAM.bam.bai:md5,159e97ddc9270c8d941f42f5553cf4fe" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-28T12:59:48.041198104" - }, "deduplication": { "content": [ [ @@ -658,27 +87,27 @@ "content": [ [ "DamagePlot_three_prime.svg", - "Length_plot_combined_data.svg", - "edit_distance.svg", "DamagePlot_five_prime.svg", - "Length_plot_forward_reverse_separated.svg", - "DamagePlot_three_prime.svg", "Length_plot_combined_data.svg", - "edit_distance.svg", - "DamagePlot_five_prime.svg", "Length_plot_forward_reverse_separated.svg", + "edit_distance.svg", "DamagePlot_three_prime.svg", + "DamagePlot_five_prime.svg", "Length_plot_combined_data.svg", + "Length_plot_forward_reverse_separated.svg", "edit_distance.svg", + "DamagePlot_three_prime.svg", "DamagePlot_five_prime.svg", - "Length_plot_forward_reverse_separated.svg" + "Length_plot_combined_data.svg", + "Length_plot_forward_reverse_separated.svg", + "edit_distance.svg" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T16:14:44.155073781" + "timestamp": "2024-07-20T06:30:49.308362955" }, "damage_estimation_log": { "content": [ @@ -717,17 +146,17 @@ "5p_freq_misincorporations.txt:md5,af2192b8a97699519d060baa3c8982fe", "DNA_comp_genome.txt:md5,0f27b55f4a7c2731f35761be4feddbfa", "DNA_composition_sample.txt:md5,1336769b56151d9de542610c4a8ef662", - "DamagePlot.pdf:md5,208a1e8fb6c6cfa2ad57cacbfa713320", - "DamagePlot_five_prime.svg:md5,46dd5d8c5ffd6c7a05d8a2e89de14250", - "DamagePlot_three_prime.svg:md5,3f3cde5cb90d8ce9e0f7d37ce198c299", - "DamageProfiler.log:md5,677886034ce239576c818eae7d000e63", - "Length_plot.pdf:md5,b2f24218c876a2fba58d45112caf1cc3", - "Length_plot_combined_data.svg:md5,69716686cbc240d1870263f014ead7d6", - "Length_plot_forward_reverse_separated.svg:md5,015fadd66539e6f0c08a2d06b8fe0b87", + "DamagePlot.pdf:md5,b378181337054a65147e9d8412ce0205", + "DamagePlot_five_prime.svg:md5,a81e11f16618d0c66a2db054dafcda69", + "DamagePlot_three_prime.svg:md5,a80745829498d374b49e069b8a1db522", + "DamageProfiler.log:md5,2eea48846d752a30a01a050d695c7ef5", + "Length_plot.pdf:md5,eaa05239076af4758a052e731d0bee8d", + "Length_plot_combined_data.svg:md5,a50415252328f10566f552cc1616667a", + "Length_plot_forward_reverse_separated.svg:md5,df44b2dc4a913262284dd04e8e6b3029", "dmgprof.json:md5,e829fb37f3e12842a6139e1d4cfe19dc", "editDistance.txt:md5,7c00cd7cc4bd87c2da4debaa2704a66a", - "edit_distance.pdf:md5,cb49b59803ccb0d12a0c93577d8931b2", - "edit_distance.svg:md5,c053e6fbe7bff9a0aa329ab6cee6c69f", + "edit_distance.pdf:md5,84ae6e86e57862c30eacdecf3b4f4b75", + "edit_distance.svg:md5,e308dba2cea9d403d7b56ad91f3ccc3a", "lgdistribution.txt:md5,3c176293ea8e58d1d56a95e693727f7a", "misincorporation.txt:md5,e25101ff61a0a3c377f8bc0252ee4451" ], @@ -738,17 +167,17 @@ "5p_freq_misincorporations.txt:md5,fc0939e3e176deef644c0bd24cb0d141", "DNA_comp_genome.txt:md5,76762da07599aff410c2ec531cd19720", "DNA_composition_sample.txt:md5,0a4d26c613bbc4541eb51ec1344d6ef4", - "DamagePlot.pdf:md5,afd9f424576f09bdd2ea243a19944f85", - "DamagePlot_five_prime.svg:md5,a674e094f2ebee3917f164050ccef1c0", - "DamagePlot_three_prime.svg:md5,e76123b06d979794576de1afca161221", - "DamageProfiler.log:md5,59e2bcffd315468c5edad541361dc3ae", - "Length_plot.pdf:md5,c3cd0ebf39f1052f5203ac21aac10139", - "Length_plot_combined_data.svg:md5,3fc70b30e528d190ea41e77e840e5b5f", - "Length_plot_forward_reverse_separated.svg:md5,befc02f6335bece8e52478d1510a4da4", + "DamagePlot.pdf:md5,b0ed12708b231ee339e3d8240d57134d", + "DamagePlot_five_prime.svg:md5,ce3fc490b874a8c383b7ac85f599bfd4", + "DamagePlot_three_prime.svg:md5,3b3c165609259d11924060ff7d49b28e", + "DamageProfiler.log:md5,2882b1207a45a0f437436a65c7dc5901", + "Length_plot.pdf:md5,8b733ed5dca91968fb2a9d78e4ddd7bd", + "Length_plot_combined_data.svg:md5,18aebba1736b7ad4e259f686540a79f4", + "Length_plot_forward_reverse_separated.svg:md5,f26a09502b21d31c1f82af2bc7224d77", "dmgprof.json:md5,49a1a9b445abf48904ead652a16fb7e4", "editDistance.txt:md5,5feeaa4b7018320fd9937e271299375c", - "edit_distance.pdf:md5,48aaa46b96a24ed51d9d38cb1cd0b1e0", - "edit_distance.svg:md5,ccb6ff8266d2de7079e4777b401126b0", + "edit_distance.pdf:md5,3c852e083cdb327e30f7cb8a68d5b339", + "edit_distance.svg:md5,8eb09a4839016d47256a2f7cf0d83c2d", "lgdistribution.txt:md5,3728eba42dd0b577a8566c103c342eb4", "misincorporation.txt:md5,a2d9fed1148fe02e372f0905c7e15b40" ], @@ -759,17 +188,17 @@ "5p_freq_misincorporations.txt:md5,8ecb71fca75a2f86cf44eb0cf4bfd269", "DNA_comp_genome.txt:md5,b78d2826f0e1be4990120105c83d0b06", "DNA_composition_sample.txt:md5,dd78c33e4d9367759e82c31247685a3b", - "DamagePlot.pdf:md5,575b78bda440ce821fec8ceabc3cf26a", - "DamagePlot_five_prime.svg:md5,acd574adb2c653f313ece6026bbc759c", - "DamagePlot_three_prime.svg:md5,8cc1343f8c1892d4bf9a6d8f1b0cf91b", - "DamageProfiler.log:md5,32d999a8090c78b0265910d66cc0ebf0", - "Length_plot.pdf:md5,2574264a49e0a589cdebd81bba10e6c2", - "Length_plot_combined_data.svg:md5,3128731a07fa197fccaadb844910821d", - "Length_plot_forward_reverse_separated.svg:md5,c299f8d1718ed5ecdb3f87e63223f826", + "DamagePlot.pdf:md5,5ced2ffb879f42c3bc102a1a7113e0ee", + "DamagePlot_five_prime.svg:md5,1283e2dc2e894b220c50e0ff435ccf6a", + "DamagePlot_three_prime.svg:md5,edcbf20a695b198187c29e872ada1173", + "DamageProfiler.log:md5,4f896a5781facc9fe1b176694127f77b", + "Length_plot.pdf:md5,7f902e5d7c43b1e20d6ea822bc28a5d9", + "Length_plot_combined_data.svg:md5,af2972902c8e9a3423c38234b99cdcd1", + "Length_plot_forward_reverse_separated.svg:md5,1d1ed566ac67069c8b12ac8ef623174f", "dmgprof.json:md5,98c584c20659b11692cbd1e280deeb97", "editDistance.txt:md5,059c352bf858c5ddb27e88253654e353", - "edit_distance.pdf:md5,38a911a75e1d29742da0b4cc802d7fb0", - "edit_distance.svg:md5,5a6b566e23f6bcee65ab5f87ea714b97", + "edit_distance.pdf:md5,7a800bda2871089c0b8dfa96007c0d29", + "edit_distance.svg:md5,422db12854ea06660b46ebc9f272c38b", "lgdistribution.txt:md5,5e8760bf271b743aa3c7c96414fb9991", "misincorporation.txt:md5,983d8fab464d67481b222aff57b06587" ], @@ -781,38 +210,18 @@ "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T16:38:34.766830902" + "timestamp": "2024-07-20T06:47:06.638043093" }, "damage_estimation_json": { "content": [ [ - "dmgprof.json", - "dmgprof.json", - "dmgprof.json" + ] ], "meta": { "nf-test": "0.8.4", "nextflow": "24.04.3" }, - "timestamp": "2024-07-19T16:21:00.793882688" - }, - "processing_fastqc_raw": { - "content": [ - [ - "JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html:md5,57632a1d575aa5874a82afdfa34efd07", - "JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.zip:md5,95a2165578924a6bdbfe35450c73b596", - "JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html:md5,1259416f24996b643197febdc878172a", - "JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.zip:md5,85ea696835a1b1eaf93d99ebb3ce97e8", - "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html:md5,8d4b1e3cf12c25d899538c21c9227b5e", - "JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip:md5,c8878ce9a00f52c2e430afadca3996d3", - "versions.yml:md5,b4672add0ce3c990afa1a2bc9f6a7c87" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-28T13:08:37.37378043" + "timestamp": "2024-07-20T06:30:49.131281277" } } \ No newline at end of file diff --git a/workflows/eager.nf b/workflows/eager.nf index c8964cec8..acffd4f4f 100644 --- a/workflows/eager.nf +++ b/workflows/eager.nf @@ -635,7 +635,9 @@ workflow EAGER { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) emit: