Fix log publishing around umitools/ umicollapse

CHANGELOG.md

@@ -27,6 +27,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1471](https://github.com/nf-core/rnaseq/pull/1471) - Fix prepare_genome subworkflow for sortmerna
 - [PR #1473](https://github.com/nf-core/rnaseq/pull/1473) - Bump STAR modules
 - [PR #1474](https://github.com/nf-core/rnaseq/pull/1474) - Bump versions to 3.18.0
+- [PR #1475](https://github.com/nf-core/rnaseq/pull/1475) - Fix log publishing around umitools/ umicollapse
 
 ## Parameters
 

docs/output.md

@@ -120,7 +120,7 @@ If multiple libraries/runs have been provided for the same sample in the input s
 
 </details>
 
-[UMI-tools](https://github.com/CGATOxford/UMI-tools) deduplicates reads based on unique molecular identifiers (UMIs) to address PCR-bias. Firstly, the UMI-tools `extract` command removes the UMI barcode information from the read sequence and adds it to the read name. Secondly, reads are deduplicated based on UMI identifier after mapping as highlighted in the [UMI-tools dedup](#umi-tools-dedup) section.
+[UMI-tools](https://github.com/CGATOxford/UMI-tools) and [UMICollapse](https://github.com/Daniel-Liu-c0deb0t/UMICollapse) deduplicate reads based on unique molecular identifiers (UMIs) to address PCR-bias. Firstly, the UMI-tools `extract` command removes the UMI barcode information from the read sequence and adds it to the read name. Secondly, reads are deduplicated based on UMI identifier after mapping as highlighted in the [UMI dedup](#umi-dedup) section.
 
 To facilitate processing of input data which has the UMI barcode already embedded in the read name from the start, `--skip_umi_extract` can be specified in conjunction with `--with_umi`.
 
@@ -305,7 +305,7 @@ The original BAM files generated by the selected alignment algorithm are further
 
 ![MultiQC - SAMtools mapped reads per contig plot](images/mqc_samtools_idxstats.png)
 
-### UMI-tools dedup
+### UMI dedup
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -314,7 +314,7 @@ The original BAM files generated by the selected alignment algorithm are further
   - `<SAMPLE>.umi_dedup.sorted.bam`: If `--save_umi_intermeds` is specified the UMI deduplicated, coordinate sorted BAM file containing read alignments will be placed in this directory.
   - `<SAMPLE>.umi_dedup.sorted.bam.bai`: If `--save_umi_intermeds` is specified the BAI index file for the UMI deduplicated, coordinate sorted BAM file will be placed in this directory.
   - `<SAMPLE>.umi_dedup.sorted.bam.csi`: If `--save_umi_intermeds --bam_csi_index` is specified the CSI index file for the UMI deduplicated, coordinate sorted BAM file will be placed in this directory.
-- `<ALIGNER>/umitools/`
+- `<ALIGNER>/umitools/` (UMI-tools only)
   - `*_edit_distance.tsv`: Reports the (binned) average edit distance between the UMIs at each position.
   - `*_per_umi.tsv`: UMI-level summary statistics.
   - `*_per_umi_per_position.tsv`: Tabulates the counts for unique combinations of UMI and position.
@@ -323,7 +323,7 @@ The content of the files above is explained in more detail in the [UMI-tools doc
 
 </details>
 
-After extracting the UMI information from the read sequence (see [UMI-tools extract](#umi-tools-extract)), the second step in the removal of UMI barcodes involves deduplicating the reads based on both mapping and UMI barcode information using the UMI-tools `dedup` command. This will generate a filtered BAM file after the removal of PCR duplicates.
+After extracting the UMI information from the read sequence (see [UMI-tools extract](#umi-tools-extract)), the second step in the removal of UMI barcodes involves deduplicating the reads based on both mapping and UMI barcode information. UMI deduplication can be carried out either with [UMI-tools](https://github.com/CGATOxford/UMI-tools) or [UMICollapse](https://github.com/Daniel-Liu-c0deb0t/UMICollapse), set via the `umi_dedup_tool` parameter. The output BAM files are the same, though UMI-tools has some additional outputs, as described above. Either method will generate a filtered BAM file after the removal of PCR duplicates.
 
 ### picard MarkDuplicates
 

tests/.nftignore

@@ -32,7 +32,7 @@ umitools/*.umi_extract.log
 {hisat2,star_rsem,star_salmon}/stringtie/*.ballgown/t_data.ctab
 {hisat2,star_rsem,star_salmon}/stringtie/*.gene.abundance.txt
 {hisat2,star_rsem,star_salmon}/stringtie/*.{coverage,transcripts}.gtf
-{hisat2,star_rsem,star_salmon}/umitools/genomic_dedup_log/*_UMICollapse.log
+{hisat2,star_rsem,star_salmon}/{umitools,umicollapse}/{genomic,transcriptomic}_dedup_log/*.log
 {multiqc,multiqc/**}/multiqc_report.html
 {multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt
 {multiqc,multiqc/**}/multiqc_report_data/hisat2_pe_plot.txt

tests/umi.nf.test

@@ -15,6 +15,7 @@ nextflow_pipeline {
                 umi_dedup_tool = 'umicollapse'
                 aligner = 'hisat2'
                 outdir = "$outputDir"
+                save_umi_intermeds = true
             }
         }
 
@@ -49,6 +50,7 @@ nextflow_pipeline {
                 umitools_dedup_stats = true
                 skip_bbsplit = true
                 outdir = "$outputDir"
+                save_umi_intermeds = true
             }
         }
 

tests/umi.nf.test.snap

@@ -612,6 +612,10 @@
                 "star_salmon/RAP1_IAA_30M_REP1",
                 "star_salmon/RAP1_IAA_30M_REP1.umi_dedup.sorted.bam",
                 "star_salmon/RAP1_IAA_30M_REP1.umi_dedup.sorted.bam.bai",
+                "star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.bam",
+                "star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.filtered.bam",
+                "star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.sorted.bam",
+                "star_salmon/RAP1_IAA_30M_REP1.umi_dedup.transcriptome.sorted.bam.bai",
                 "star_salmon/RAP1_IAA_30M_REP1/aux_info",
                 "star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv",
                 "star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz",
@@ -629,6 +633,9 @@
                 "star_salmon/RAP1_UNINDUCED_REP1",
                 "star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.sorted.bam",
                 "star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.sorted.bam.bai",
+                "star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.bam",
+                "star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.sorted.bam",
+                "star_salmon/RAP1_UNINDUCED_REP1.umi_dedup.transcriptome.sorted.bam.bai",
                 "star_salmon/RAP1_UNINDUCED_REP1/aux_info",
                 "star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv",
                 "star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz",
@@ -646,6 +653,9 @@
                 "star_salmon/RAP1_UNINDUCED_REP2",
                 "star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.sorted.bam",
                 "star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.sorted.bam.bai",
+                "star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.bam",
+                "star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.sorted.bam",
+                "star_salmon/RAP1_UNINDUCED_REP2.umi_dedup.transcriptome.sorted.bam.bai",
                 "star_salmon/RAP1_UNINDUCED_REP2/aux_info",
                 "star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv",
                 "star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz",
@@ -663,6 +673,10 @@
                 "star_salmon/WT_REP1",
                 "star_salmon/WT_REP1.umi_dedup.sorted.bam",
                 "star_salmon/WT_REP1.umi_dedup.sorted.bam.bai",
+                "star_salmon/WT_REP1.umi_dedup.transcriptome.bam",
+                "star_salmon/WT_REP1.umi_dedup.transcriptome.filtered.bam",
+                "star_salmon/WT_REP1.umi_dedup.transcriptome.sorted.bam",
+                "star_salmon/WT_REP1.umi_dedup.transcriptome.sorted.bam.bai",
                 "star_salmon/WT_REP1/aux_info",
                 "star_salmon/WT_REP1/aux_info/ambig_info.tsv",
                 "star_salmon/WT_REP1/aux_info/expected_bias.gz",
@@ -680,6 +694,10 @@
                 "star_salmon/WT_REP2",
                 "star_salmon/WT_REP2.umi_dedup.sorted.bam",
                 "star_salmon/WT_REP2.umi_dedup.sorted.bam.bai",
+                "star_salmon/WT_REP2.umi_dedup.transcriptome.bam",
+                "star_salmon/WT_REP2.umi_dedup.transcriptome.filtered.bam",
+                "star_salmon/WT_REP2.umi_dedup.transcriptome.sorted.bam",
+                "star_salmon/WT_REP2.umi_dedup.transcriptome.sorted.bam.bai",
                 "star_salmon/WT_REP2/aux_info",
                 "star_salmon/WT_REP2/aux_info/ambig_info.tsv",
                 "star_salmon/WT_REP2/aux_info/expected_bias.gz",
@@ -1261,10 +1279,18 @@
                 "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt",
                 "umitools",
                 "umitools/RAP1_IAA_30M_REP1.umi_extract.log",
+                "umitools/RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz",
+                "umitools/RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz",
+                "umitools/RAP1_UNINDUCED_REP1.umi_extract.fastq.gz",
                 "umitools/RAP1_UNINDUCED_REP1.umi_extract.log",
+                "umitools/RAP1_UNINDUCED_REP2.umi_extract.fastq.gz",
                 "umitools/RAP1_UNINDUCED_REP2.umi_extract.log",
                 "umitools/WT_REP1.umi_extract.log",
-                "umitools/WT_REP2.umi_extract.log"
+                "umitools/WT_REP1.umi_extract_1.fastq.gz",
+                "umitools/WT_REP1.umi_extract_2.fastq.gz",
+                "umitools/WT_REP2.umi_extract.log",
+                "umitools/WT_REP2.umi_extract_1.fastq.gz",
+                "umitools/WT_REP2.umi_extract_2.fastq.gz"
             ],
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
@@ -1467,14 +1493,22 @@
                 "WT_REP2.umi_dedup.sorted_per_umi_per_position.tsv:md5,6f5656947a7f0076df446e6f40430027",
                 "WT_REP2.umi_dedup.transcriptome.sorted_edit_distance.tsv:md5,3e3c6a7e8996e566350742e9911366d3",
                 "WT_REP2.umi_dedup.transcriptome.sorted_per_umi.tsv:md5,0c986c4cb7a77f650a19e2c454b9b179",
-                "WT_REP2.umi_dedup.transcriptome.sorted_per_umi_per_position.tsv:md5,af9028dbdab81de3854a32cd1d19ac8b"
+                "WT_REP2.umi_dedup.transcriptome.sorted_per_umi_per_position.tsv:md5,af9028dbdab81de3854a32cd1d19ac8b",
+                "RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,e83d7f738fbbfaa541a2e71fe4663447",
+                "RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,4f2873cbf584d6e84187238a4ae2b8fa",
+                "RAP1_UNINDUCED_REP1.umi_extract.fastq.gz:md5,9e42242fd68baac592140f63a8a716ce",
+                "RAP1_UNINDUCED_REP2.umi_extract.fastq.gz:md5,5a92b642927b8603c4765e5305e23e9c",
+                "WT_REP1.umi_extract_1.fastq.gz:md5,f312fac9c384a889ae4f959839263604",
+                "WT_REP1.umi_extract_2.fastq.gz:md5,ffca24924108fd54151620b7538b9e1a",
+                "WT_REP2.umi_extract_1.fastq.gz:md5,c3180451a24ce51fc35c1684521ae287",
+                "WT_REP2.umi_extract_2.fastq.gz:md5,067ff23f8d1307ad241cd70bc186b5c1"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-11T18:07:55.751564456"
+        "timestamp": "2024-12-20T00:02:04.611696704"
     },
     "Params: --aligner hisat2 --umi_dedup_tool 'umicollapse'": {
         "content": [
@@ -2130,13 +2164,13 @@
                 "hisat2/stringtie/WT_REP2.coverage.gtf",
                 "hisat2/stringtie/WT_REP2.gene.abundance.txt",
                 "hisat2/stringtie/WT_REP2.transcripts.gtf",
-                "hisat2/umitools",
-                "hisat2/umitools/genomic_dedup_log",
-                "hisat2/umitools/genomic_dedup_log/RAP1_IAA_30M_REP1.umi_dedup.sorted_UMICollapse.log",
-                "hisat2/umitools/genomic_dedup_log/RAP1_UNINDUCED_REP1.umi_dedup.sorted_UMICollapse.log",
-                "hisat2/umitools/genomic_dedup_log/RAP1_UNINDUCED_REP2.umi_dedup.sorted_UMICollapse.log",
-                "hisat2/umitools/genomic_dedup_log/WT_REP1.umi_dedup.sorted_UMICollapse.log",
-                "hisat2/umitools/genomic_dedup_log/WT_REP2.umi_dedup.sorted_UMICollapse.log",
+                "hisat2/umicollapse",
+                "hisat2/umicollapse/genomic_dedup_log",
+                "hisat2/umicollapse/genomic_dedup_log/RAP1_IAA_30M_REP1.umi_dedup.sorted_UMICollapse.log",
+                "hisat2/umicollapse/genomic_dedup_log/RAP1_UNINDUCED_REP1.umi_dedup.sorted_UMICollapse.log",
+                "hisat2/umicollapse/genomic_dedup_log/RAP1_UNINDUCED_REP2.umi_dedup.sorted_UMICollapse.log",
+                "hisat2/umicollapse/genomic_dedup_log/WT_REP1.umi_dedup.sorted_UMICollapse.log",
+                "hisat2/umicollapse/genomic_dedup_log/WT_REP2.umi_dedup.sorted_UMICollapse.log",
                 "multiqc",
                 "multiqc/hisat2",
                 "multiqc/hisat2/multiqc_report.html",
@@ -2548,10 +2582,18 @@
                 "trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt",
                 "umitools",
                 "umitools/RAP1_IAA_30M_REP1.umi_extract.log",
+                "umitools/RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz",
+                "umitools/RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz",
+                "umitools/RAP1_UNINDUCED_REP1.umi_extract.fastq.gz",
                 "umitools/RAP1_UNINDUCED_REP1.umi_extract.log",
+                "umitools/RAP1_UNINDUCED_REP2.umi_extract.fastq.gz",
                 "umitools/RAP1_UNINDUCED_REP2.umi_extract.log",
                 "umitools/WT_REP1.umi_extract.log",
-                "umitools/WT_REP2.umi_extract.log"
+                "umitools/WT_REP1.umi_extract_1.fastq.gz",
+                "umitools/WT_REP1.umi_extract_2.fastq.gz",
+                "umitools/WT_REP2.umi_extract.log",
+                "umitools/WT_REP2.umi_extract_1.fastq.gz",
+                "umitools/WT_REP2.umi_extract_2.fastq.gz"
             ],
             [
                 "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055",
@@ -2688,14 +2730,22 @@
                 "cmd_info.json:md5,809380ddce725a8fab75dd7741b64bf6",
                 "lib_format_counts.json:md5,d231ba7624b67eb654989f69530e2925",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
-                "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
+                "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe",
+                "RAP1_IAA_30M_REP1.umi_extract_1.fastq.gz:md5,e83d7f738fbbfaa541a2e71fe4663447",
+                "RAP1_IAA_30M_REP1.umi_extract_2.fastq.gz:md5,4f2873cbf584d6e84187238a4ae2b8fa",
+                "RAP1_UNINDUCED_REP1.umi_extract.fastq.gz:md5,9e42242fd68baac592140f63a8a716ce",
+                "RAP1_UNINDUCED_REP2.umi_extract.fastq.gz:md5,5a92b642927b8603c4765e5305e23e9c",
+                "WT_REP1.umi_extract_1.fastq.gz:md5,f312fac9c384a889ae4f959839263604",
+                "WT_REP1.umi_extract_2.fastq.gz:md5,ffca24924108fd54151620b7538b9e1a",
+                "WT_REP2.umi_extract_1.fastq.gz:md5,c3180451a24ce51fc35c1684521ae287",
+                "WT_REP2.umi_extract_2.fastq.gz:md5,067ff23f8d1307ad241cd70bc186b5c1"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-11T18:01:45.228731692"
+        "timestamp": "2024-12-19T22:33:42.012684597"
     },
     "--umi_dedup_tool 'umitools - stub": {
         "content": [
@@ -2804,9 +2854,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-11T18:08:48.404716766"
+        "timestamp": "2024-12-19T23:28:01.570835895"
     }
-}
+}