More sorting fixes

Author: pinin4fjords

tests/default.nf.test.snap

@@ -699,8 +699,6 @@
                 "salmon/WT_REP2/logs/salmon_quant.log",
                 "salmon/WT_REP2/quant.genes.sf",
                 "salmon/WT_REP2/quant.sf",
-                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
-                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/deseq2_qc",
                 "salmon/deseq2_qc/R_sessionInfo.log",
                 "salmon/deseq2_qc/deseq2.dds.RData",
@@ -714,11 +712,13 @@
                 "salmon/deseq2_qc/size_factors/WT_REP1.txt",
                 "salmon/deseq2_qc/size_factors/WT_REP2.txt",
                 "salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
+                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
                 "salmon/salmon.merged.gene_counts.tsv",
                 "salmon/salmon.merged.gene_counts_length_scaled.tsv",
                 "salmon/salmon.merged.gene_counts_scaled.tsv",
                 "salmon/salmon.merged.gene_lengths.tsv",
                 "salmon/salmon.merged.gene_tpm.tsv",
+                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/salmon.merged.transcript_counts.tsv",
                 "salmon/salmon.merged.transcript_lengths.tsv",
                 "salmon/salmon.merged.transcript_tpm.tsv",

tests/featurecounts_group_type.nf.test.snap

@@ -686,8 +686,6 @@
                 "salmon/WT_REP2/logs/salmon_quant.log",
                 "salmon/WT_REP2/quant.genes.sf",
                 "salmon/WT_REP2/quant.sf",
-                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
-                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/deseq2_qc",
                 "salmon/deseq2_qc/R_sessionInfo.log",
                 "salmon/deseq2_qc/deseq2.dds.RData",
@@ -701,11 +699,13 @@
                 "salmon/deseq2_qc/size_factors/WT_REP1.txt",
                 "salmon/deseq2_qc/size_factors/WT_REP2.txt",
                 "salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
+                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
                 "salmon/salmon.merged.gene_counts.tsv",
                 "salmon/salmon.merged.gene_counts_length_scaled.tsv",
                 "salmon/salmon.merged.gene_counts_scaled.tsv",
                 "salmon/salmon.merged.gene_lengths.tsv",
                 "salmon/salmon.merged.gene_tpm.tsv",
+                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/salmon.merged.transcript_counts.tsv",
                 "salmon/salmon.merged.transcript_lengths.tsv",
                 "salmon/salmon.merged.transcript_tpm.tsv",

tests/min_mapped_reads.nf.test.snap

@@ -602,8 +602,6 @@
                 "salmon/WT_REP2/logs/salmon_quant.log",
                 "salmon/WT_REP2/quant.genes.sf",
                 "salmon/WT_REP2/quant.sf",
-                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
-                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/deseq2_qc",
                 "salmon/deseq2_qc/R_sessionInfo.log",
                 "salmon/deseq2_qc/deseq2.dds.RData",
@@ -617,11 +615,13 @@
                 "salmon/deseq2_qc/size_factors/WT_REP1.txt",
                 "salmon/deseq2_qc/size_factors/WT_REP2.txt",
                 "salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
+                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
                 "salmon/salmon.merged.gene_counts.tsv",
                 "salmon/salmon.merged.gene_counts_length_scaled.tsv",
                 "salmon/salmon.merged.gene_counts_scaled.tsv",
                 "salmon/salmon.merged.gene_lengths.tsv",
                 "salmon/salmon.merged.gene_tpm.tsv",
+                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/salmon.merged.transcript_counts.tsv",
                 "salmon/salmon.merged.transcript_lengths.tsv",
                 "salmon/salmon.merged.transcript_tpm.tsv",

tests/umi.nf.test.snap

@@ -591,8 +591,6 @@
                 "salmon/WT_REP2/logs/salmon_quant.log",
                 "salmon/WT_REP2/quant.genes.sf",
                 "salmon/WT_REP2/quant.sf",
-                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
-                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/deseq2_qc",
                 "salmon/deseq2_qc/R_sessionInfo.log",
                 "salmon/deseq2_qc/deseq2.dds.RData",
@@ -606,11 +604,13 @@
                 "salmon/deseq2_qc/size_factors/WT_REP1.txt",
                 "salmon/deseq2_qc/size_factors/WT_REP2.txt",
                 "salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
+                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
                 "salmon/salmon.merged.gene_counts.tsv",
                 "salmon/salmon.merged.gene_counts_length_scaled.tsv",
                 "salmon/salmon.merged.gene_counts_scaled.tsv",
                 "salmon/salmon.merged.gene_lengths.tsv",
                 "salmon/salmon.merged.gene_tpm.tsv",
+                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/salmon.merged.transcript_counts.tsv",
                 "salmon/salmon.merged.transcript_lengths.tsv",
                 "salmon/salmon.merged.transcript_tpm.tsv",
@@ -2543,8 +2543,6 @@
                 "salmon/WT_REP2/logs/salmon_quant.log",
                 "salmon/WT_REP2/quant.genes.sf",
                 "salmon/WT_REP2/quant.sf",
-                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
-                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/deseq2_qc",
                 "salmon/deseq2_qc/R_sessionInfo.log",
                 "salmon/deseq2_qc/deseq2.dds.RData",
@@ -2558,11 +2556,13 @@
                 "salmon/deseq2_qc/size_factors/WT_REP1.txt",
                 "salmon/deseq2_qc/size_factors/WT_REP2.txt",
                 "salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
+                "salmon/salmon.merged.gene.SummarizedExperiment.rds",
                 "salmon/salmon.merged.gene_counts.tsv",
                 "salmon/salmon.merged.gene_counts_length_scaled.tsv",
                 "salmon/salmon.merged.gene_counts_scaled.tsv",
                 "salmon/salmon.merged.gene_lengths.tsv",
                 "salmon/salmon.merged.gene_tpm.tsv",
+                "salmon/salmon.merged.transcript.SummarizedExperiment.rds",
                 "salmon/salmon.merged.transcript_counts.tsv",
                 "salmon/salmon.merged.transcript_lengths.tsv",
                 "salmon/salmon.merged.transcript_tpm.tsv",