Apply suggestions from code review

Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>

.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.

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)
 

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 {

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

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`.
 

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'

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() )