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Update pipeline-level tests
1 parent f59132a commit 40f05c5

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+81
-81
lines changed

‎tests/default.nf.test.snap‎

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@@ -37,7 +37,7 @@
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},
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"cutadapt": 4.9
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"UNTAR_SALMON_INDEX": {
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"untar": 1.34
@@ -90,7 +90,7 @@
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T18:47:30.454374101"
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"timestamp": "2024-10-23T10:43:40.33664602"
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},
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"Params: default": {
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"content": [
@@ -212,7 +212,7 @@
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},
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"TRIMGALORE": {
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"trimgalore": "0.6.10",
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"cutadapt": 4.2
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"cutadapt": 4.9
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},
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"TXIMETA_TXIMPORT": {
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"bioconductor-tximeta": "1.20.1"
@@ -1300,18 +1300,18 @@
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"fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
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1303-
"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
1303+
"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878",
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"fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
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"fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
13061306
"fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
13071307
"fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
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"fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
1309-
"fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
1310-
"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
1309+
"fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f",
1310+
"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db",
13111311
"multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0",
1312-
"multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa",
1312+
"multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b",
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"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
1314-
"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
1314+
"multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97",
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"multiqc_featurecounts_biotype_plot.txt:md5,5d83930a8c0aebf5fff0a5d12857b42d",
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"multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c",
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"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1459,6 +1459,6 @@
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T19:14:46.845308285"
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"timestamp": "2024-10-23T10:42:45.202573855"
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}
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}

‎tests/featurecounts_group_type.nf.test.snap‎

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@@ -37,7 +37,7 @@
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},
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"nextflow": "24.04.4"
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"timestamp": "2024-10-21T18:52:01.516368536"
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"timestamp": "2024-10-23T10:54:29.62339584"
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},
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"Params: --featurecounts_group_type false": {
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"content": [
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"TXIMETA_TXIMPORT": {
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"bioconductor-tximeta": "1.20.1"
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"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878",
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"fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
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"fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
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"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
1275+
"fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f",
1276+
"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db",
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"multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0",
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"multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa",
1278+
"multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b",
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"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97",
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"multiqc_samtools_idxstats.txt:md5,8b8f6cb092004918c18319a8cd64eb4c",
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"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1409,6 +1409,6 @@
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T19:24:36.371474446"
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"timestamp": "2024-10-23T10:53:28.969150716"
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}
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}

‎tests/hisat2.nf.test.snap‎

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},
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"TRIMGALORE": {
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"trimgalore": "0.6.10",
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"cutadapt": 4.9
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"UNTAR_HISAT2_INDEX": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-23T11:01:31.33505759"
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},
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"Params: --aligner hisat2": {
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"content": [
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"TXIMETA_TXIMPORT": {
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"bioconductor-tximeta": "1.20.1"
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"fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
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"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
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"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878",
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"fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
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"fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
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"fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
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"fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
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"fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
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"fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
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"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
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"fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f",
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"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db",
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"multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e",
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"multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa",
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"multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b",
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"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97",
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"multiqc_featurecounts_biotype_plot.txt:md5,d784fc4b2dce860c8f88cc3e936e589e",
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"multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49",
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"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-23T11:00:43.422573373"
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}
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}

‎tests/kallisto.nf.test.snap‎

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},
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"TRIMGALORE": {
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"cutadapt": 4.9
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"bioconductor-tximeta": "1.20.1"
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"cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c",
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"fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
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"fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
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"fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
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"fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
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"fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
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"fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f",
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"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233"
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"multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97"
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]
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-21T15:46:36.506804194"
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"timestamp": "2024-10-23T11:04:57.579312846"
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},
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"Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": {
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"timestamp": "2024-10-23T11:05:54.052864085"
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}
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}

‎tests/min_mapped_reads.nf.test.snap‎

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"multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
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"timestamp": "2024-10-23T11:19:22.443482528"
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}
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}

‎tests/remove_ribo_rna.nf.test.snap‎

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"TRIMGALORE": {
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"trimgalore": "0.6.10",
128-
"cutadapt": 4.2
128+
"cutadapt": 4.9
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},
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"TXIMETA_TXIMPORT": {
131131
"bioconductor-tximeta": "1.20.1"
@@ -1227,18 +1227,18 @@
12271227
"fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
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"fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
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"fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
1230-
"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
1230+
"fastqc_trimmed_overrepresented_sequences_plot.txt:md5,c755e9d044ea1a82b2c8edde867b4878",
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"fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e",
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"fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5",
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"fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a",
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"fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037",
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"fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
1236-
"fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
1237-
"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
1236+
"fastqc_trimmed_sequence_counts_plot.txt:md5,9fd642bdd1da354f296bb8092205608f",
1237+
"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,0758257b497283b1ef28171e694db6db",
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"multiqc_citations.txt:md5,bfa9fd61367cd7265e324d009c974778",
1239-
"multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa",
1239+
"multiqc_cutadapt.txt:md5,583b7b9ba76b26162bb9610ed746454b",
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"multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,54743154d0e8858980acffeb5b6f6a97",
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"multiqc_featurecounts_biotype_plot.txt:md5,f4de303d3277d862031df94b509527ba",
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"multiqc_samtools_idxstats.txt:md5,58f19b28617037a2825f812d58d55e2e",
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"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -1386,7 +1386,7 @@
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-22T12:24:58.795267716"
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"timestamp": "2024-10-23T11:36:09.902195192"
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},
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"Params: --remove_ribo_rna - stub": {
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"content": [
@@ -1429,7 +1429,7 @@
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},
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"TRIMGALORE": {
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"trimgalore": "0.6.10",
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"cutadapt": 4.2
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"cutadapt": 4.9
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},
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"UNTAR_SALMON_INDEX": {
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"untar": 1.34
@@ -1482,6 +1482,6 @@
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-22T12:26:10.797017969"
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"timestamp": "2024-10-23T11:37:11.90905171"
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}
14871487
}

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