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maxulyssemaxulysse
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update tests
1 parent 1ad7865 commit 056ce81

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8 files changed

+264
-261
lines changed

8 files changed

+264
-261
lines changed

‎tests/default.nf.test‎

Lines changed: 27 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -93,9 +93,7 @@ nextflow_pipeline {
9393
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"),
9494
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"),
9595
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"),
96-
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"),
9796
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"),
98-
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"),
9997
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"),
10098
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"),
10199
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"),
@@ -106,7 +104,6 @@ nextflow_pipeline {
106104
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"),
107105
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"),
108106
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"),
109-
path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"),
110107
// These files are not stable
111108
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name,
112109
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name,
@@ -116,6 +113,7 @@ nextflow_pipeline {
116113
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name,
117114
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name,
118115
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name,
116+
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name,
119117
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name,
120118
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name,
121119
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name,
@@ -138,6 +136,7 @@ nextflow_pipeline {
138136
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name,
139137
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name,
140138
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name,
139+
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name,
141140
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name,
142141
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name,
143142
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name,
@@ -157,6 +156,7 @@ nextflow_pipeline {
157156
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name,
158157
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name,
159158
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name,
159+
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name,
160160
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name,
161161
file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name
162162
).match("multiqc_data") },
@@ -184,8 +184,6 @@ nextflow_pipeline {
184184
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"),
185185
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"),
186186
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"),
187-
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"),
188-
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"),
189187
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"),
190188
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"),
191189
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"),
@@ -196,8 +194,6 @@ nextflow_pipeline {
196194
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"),
197195
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"),
198196
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"),
199-
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"),
200-
path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"),
201197
// PDFs, SVGs, some PNGs and HTML reports are not stable
202198
file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name,
203199
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name,
@@ -282,6 +278,8 @@ nextflow_pipeline {
282278
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name,
283279
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name,
284280
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name,
281+
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name,
282+
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name,
285283
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name,
286284
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name,
287285
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name,
@@ -302,6 +300,8 @@ nextflow_pipeline {
302300
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name,
303301
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name,
304302
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name,
303+
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name,
304+
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name,
305305
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name,
306306
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name,
307307
file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name,
@@ -754,36 +754,36 @@ nextflow_pipeline {
754754
file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name
755755
).match("star_salmon/salmon") },
756756
{ assert snapshot(
757-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"),
758-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"),
759-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"),
760-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"),
761-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"),
762-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"),
763-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"),
764-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"),
765-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"),
766-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"),
767-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"),
768-
path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"),
769-
path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"),
770-
path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"),
771-
path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"),
772-
path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"),
773-
path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"),
774-
path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"),
775-
path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"),
776-
path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"),
777757
// These files are not stable
758+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name,
759+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name,
778760
file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name,
761+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name,
762+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name,
779763
file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name,
764+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name,
765+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name,
780766
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name,
767+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name,
768+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name,
781769
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name,
770+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name,
771+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name,
782772
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name,
773+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name,
774+
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name,
783775
file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name,
776+
file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name,
777+
file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name,
784778
file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name,
779+
file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name,
780+
file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name,
785781
file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name,
782+
file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name,
783+
file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name,
786784
file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name,
785+
file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name,
786+
file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name,
787787
file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name
788788
).match("star_salmon/samtools_stats") },
789789
{ assert snapshot(

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