[skip ci] Update snaps for --pseudo_aligner salmon --skip_qc --skip_alignment

Author: pinin4fjords

tests/salmon.nf.test.snap

@@ -4,22 +4,22 @@
             34,
             {
                 "BBMAP_BBSPLIT": {
-                    "bbmap": 39.01
+                    "bbmap": 39.1
                 },
                 "CAT_FASTQ": {
-                    "cat": 8.3
+                    "cat": 9.5
                 },
                 "CUSTOM_CATADDITIONALFASTA": {
-                    "python": "3.9.5"
+                    "python": "3.12.2"
                 },
                 "CUSTOM_GETCHROMSIZES": {
-                    "getchromsizes": 1.2
+                    "getchromsizes": 1.21
                 },
                 "CUSTOM_TX2GENE": {
-                    "python": "3.9.5"
+                    "python": "3.10.4"
                 },
                 "FQ_SUBSAMPLE": {
-                    "fq": "0.9.1 (2022-02-22)"
+                    "fq": "0.12.0 (2024-07-08)"
                 },
                 "GTF2BED": {
                     "perl": "5.26.2"
@@ -34,14 +34,14 @@
                     "gunzip": 1.1
                 },
                 "SALMON_QUANT": {
-                    "salmon": "1.10.1"
+                    "salmon": "1.10.3"
                 },
                 "SE_GENE": {
                     "bioconductor-summarizedexperiment": "1.32.0"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "0.6.7",
-                    "cutadapt": 3.4
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.2
                 },
                 "TXIMETA_TXIMPORT": {
                     "bioconductor-tximeta": "1.20.1"
@@ -290,62 +290,62 @@
                 "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
                 "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
                 "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150",
-                "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
+                "multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa",
                 "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
                 "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
-                "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c",
+                "cmd_info.json:md5,138b27764a97d468418b3dac5e7f1cef",
                 "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1",
                 "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
-                "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636",
+                "cmd_info.json:md5,87bcf1e84fc31a794e3c8f8b227d11c3",
                 "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935",
                 "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
-                "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326",
+                "cmd_info.json:md5,ec504469f9b0e33c94f85846f1486d7f",
                 "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3",
                 "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
-                "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d",
+                "cmd_info.json:md5,591436d401b6df6f3c6a8b16913158f4",
                 "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6",
                 "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f",
                 "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20",
                 "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
                 "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56",
-                "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac",
+                "cmd_info.json:md5,fe66c9d876645b9260d8c2488157d4d4",
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.0"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-10T07:25:22.063836"
+        "timestamp": "2024-10-21T16:22:14.604923669"
     },
     "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": {
         "content": [
             16,
             {
                 "BBMAP_BBSPLIT": {
-                    "bbmap": 39.01
+                    "bbmap": 39.1
                 },
                 "CAT_FASTQ": {
-                    "cat": 8.3
+                    "cat": 9.5
                 },
                 "CUSTOM_CATADDITIONALFASTA": {
                     "python": null
                 },
                 "CUSTOM_GETCHROMSIZES": {
-                    "getchromsizes": 1.2
+                    "getchromsizes": 1.21
                 },
                 "GTF2BED": {
                     "perl": "5.26.2"
@@ -360,8 +360,8 @@
                     "gunzip": 1.1
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "0.6.7",
-                    "cutadapt": 3.4
+                    "trimgalore": "0.6.10",
+                    "cutadapt": 4.2
                 },
                 "UNTAR_SALMON_INDEX": {
                     "untar": 1.34
@@ -400,8 +400,8 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.09.0"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-10T07:07:48.845197"
+        "timestamp": "2024-10-21T16:23:12.380483903"
     }
-}
+}