Apply suggestions from code review

Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
1 year ago · 6c2ce4a1c9
parent 0c9d6cabe8
commit 6c2ce4a1c9
7 changed files with 16 additions and 14 deletions
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/taxp

 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/taxprofiler/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/taxprofiler _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/taxprofiler/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/taxprofiler _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
--- a/CITATIONS.md
+++ b/CITATIONS.md
@ -62,7 +62,7 @@

  > Breitwieser, Florian P., Daniel N. Baker, and Steven L. Salzberg. 2018. KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biology 19 (1): 198. doi: 10.1186/s13059-018-1568-0

-  - [MetaPhlAn3](https://doi.org/10.7554/eLife.65088)
+- [MetaPhlAn3](https://doi.org/10.7554/eLife.65088)

  > Beghini, Francesco, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, et al. 2021. “Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse Microbial Communities with BioBakery 3.” Edited by Peter Turnbaugh, Eduardo Franco, and C Titus Brown. ELife 10 (May): e65088. doi: 10.7554/eLife.65088

@ -76,7 +76,7 @@

 - [DIAMOND](https://doi.org/10.1038/nmeth.3176)

-> Buchfink, Benjamin, Chao Xie, and Daniel H. Huson. 2015. “Fast and Sensitive Protein Alignment Using DIAMOND.” Nature Methods 12 (1): 59-60. doi: 10.1038/nmeth.3176.
+  > Buchfink, Benjamin, Chao Xie, and Daniel H. Huson. 2015. “Fast and Sensitive Protein Alignment Using DIAMOND.” Nature Methods 12 (1): 59-60. doi: 10.1038/nmeth.3176.

 - [Centrifuge](https://doi.org/10.1101/gr.210641.116)

--- a/conf/test_krakenuniq.config
+++ b/conf/test_krakenuniq.config
@ -45,10 +45,11 @@ params {
    run_motus                             = false
    run_krona                             = true
    krona_taxonomy_directory              = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
-    malt_save_reads                       = true
-    kraken2_save_reads                    = true
-    centrifuge_save_reads                 = true
-    diamond_save_reads                    = true
+    malt_save_reads                       = false
+    kraken2_save_reads                    = false
+    centrifuge_save_reads                 = false
+    diamond_save_reads                    = false
+    run_profile_standardisation           = true
 }

 process {
--- a/docs/output.md
+++ b/docs/output.md
@ -16,12 +16,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [AdapterRemoval](#adapterremoval) - Adapter trimming for Illumina data
 - [Porechop](#porechop) - Adapter removal for Oxford Nanopore data
 - [BBDuk](#bbduk) - Quality trimming and filtering for Illumina data
- [PRINSEQ++](#prinseq++) - Quality trimming and filtering for Illunina data
+- [PRINSEQ++](#prinseq) - Quality trimming and filtering for Illunina data
 - [Filtlong](#filtlong) - Quality trimming and filtering for Nanopore data
 - [Bowtie2](#bowtie2) - Host removal for Illumina reads
 - [minimap2](#minimap2) - Host removal for Nanopore reads
- [SAMtools stats](#samtoolsstats) - Statistics from host removal
- [SAMtools bam2fq](#samtoolsfastq) - Converts unmapped BAM file to fastq format (minimap2 only)
+- [SAMtools stats](#samtools-stats) - Statistics from host removal
+- [SAMtools bam2fq](#samtools-fastq) - Converts unmapped BAM file to fastq format (minimap2 only)
 - [Bracken](#bracken) - Taxonomic classifier using k-mers and abundance estimations
 - [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches
 - [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species
--- a/docs/usage.md
+++ b/docs/usage.md
@ -199,7 +199,7 @@ You can optionally save the FASTQ output of the run merging with the `--save_com

 > ⚠️ For nanopore data: we do not recommend performing any read preprocessing or complexity filtering if you are using ONTs Guppy toolkit for basecalling and post-processing.

-#### Host Removal
+#### Host-Read Removal

 Removal of possible-host reads from FASTQ files prior classification/profiling can be activated with `--perform_shortread_hostremoval` or `--perform_longread_hostremoval`.

--- a/nextflow.config
+++ b/nextflow.config
@ -102,7 +102,7 @@ params {
    shortread_hostremoval_index            = null
    longread_hostremoval_index             = null
    save_hostremoval_index                 = false
-    save_hostremoval_bam                = false
+    save_hostremoval_bam                  = false
    save_hostremoval_unmapped              = false


@ -302,7 +302,7 @@ manifest {
    name            = 'nf-core/taxprofiler'
    author          = """nf-core community"""
    homePage        = 'https://github.com/nf-core/taxprofiler'
-    description     = """Taxonomic profiling of shotgun metagenomic data"""
+    description     = """Taxonomic classification and profiling of shotgun metagenomic data"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=22.10.1'
    version = '1.0.0'
--- a/subworkflows/local/profiling.nf
+++ b/subworkflows/local/profiling.nf
@ -329,7 +329,7 @@ workflow PROFILING {
                                            reads: [ single_meta + db_meta, reads.flatten() ]
                                            db: db
                                }
-        // Hardcode to _always_ produce the report file (which is our basic otput, and goes into)
+        // Hardcode to _always_ produce the report file (which is our basic output, and goes into)
        KRAKENUNIQ_PRELOADEDKRAKENUNIQ ( ch_input_for_krakenuniq.reads, ch_input_for_krakenuniq.db, params.krakenuniq_ram_chunk_size, params.krakenuniq_save_reads, true, params.krakenuniq_save_readclassifications )
        ch_multiqc_files       = ch_multiqc_files.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report )
        ch_versions            = ch_versions.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.versions.first() )