Start adding framework for altenrative host-removal tools

.nf-test.log

@@ -0,0 +1,18 @@
+Sept-18 10:36:37.957 [main] INFO  com.askimed.nf.test.App - nf-test 0.9.2
+Sept-18 10:36:38.004 [main] INFO  com.askimed.nf.test.App - Arguments: [test, --tag, test, --profile, +docker, --update-snapshot]
+Sept-18 10:36:39.635 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 25.04.7
+Sept-18 10:36:39.637 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Load config from file /home/james/git/nf-core/taxprofiler/nf-test.config...
+Sept-18 10:36:40.773 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 78 files from directory /home/james/git/nf-core/taxprofiler in 0.241 sec
+Sept-18 10:36:40.775 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
+Sept-18 10:36:40.775 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/home/james/git/nf-core/taxprofiler/tests/default.nf.test]
+Sept-18 10:36:41.445 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
+Sept-18 10:36:41.446 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
+Sept-18 10:36:41.447 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test pipeline' from file '/home/james/git/nf-core/taxprofiler/tests/default.nf.test'.
+Sept-18 10:36:41.447 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test 'c20badfb: -profile test'. type: com.askimed.nf.test.lang.pipeline.PipelineTest
+Sept-18 10:54:39.228 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Load snapshots from file '/home/james/git/nf-core/taxprofiler/tests/default.nf.test.snap'
+Sept-18 10:54:39.343 [main] DEBUG com.askimed.nf.test.lang.extensions.Snapshot - Snapshots '-profile test' do not match. Update snapshots flag set.
+Sept-18 10:54:39.343 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Updated snapshot '-profile test'
+Sept-18 10:54:39.359 [main] DEBUG com.askimed.nf.test.lang.extensions.SnapshotFile - Wrote snapshots to file '/home/james/git/nf-core/taxprofiler/tests/default.nf.test.snap'
+Sept-18 10:54:39.359 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test 'c20badfb: -profile test' finished. status: PASSED
+Sept-18 10:54:39.364 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test pipeline' finished. snapshot file: true, skipped tests: false, failed tests: false
+Sept-18 10:54:39.370 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 0 tests failed. Done!

CITATIONS.md

@@ -69,6 +69,10 @@
 
   > Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2). https://doi.org/10.1093/gigascience/giab008
 
+- [Hostile](https://doi.org/10.1093/bioinformatics/btad728)
+
+  > Constantinides, B., Hunt, M., Crook, D.W., 2023. Hostile: accurate decontamination of microbial host sequences. Bioinformatics 39. https://doi.org/10.1093/bioinformatics/btad728
+
 - [Bracken](https://doi.org/10.7717/peerj-cs.104)
 
   > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ. Computer Science, 3(e104), e104. https://doi.org/10.7717/peerj-cs.104

README.md

@@ -32,7 +32,7 @@
 2. Performs optional read pre-processing
    - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop), [Porechop_ABI](https://github.com/bonsai-team/Porechop_ABI))
    - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)), [Nanoq](https://github.com/esteinig/nanoq)
-   - Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2))
+   - Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2), both: [Hostile](https://github.com/bede/hostile)),
    - Run merging
 3. Supports statistics metagenome coverage estimation ([Nonpareil](https://nonpareil.readthedocs.io/en/latest/)) and for host-read removal ([Samtools](http://www.htslib.org/))
 4. Performs taxonomic classification and/or profiling using one or more of:

assets/multiqc_config.yml

@@ -38,6 +38,8 @@ report_section_order:
     order: 200
   samtools:
     order: 100
+  hostile:
+    order: 95
   kraken:
     order: 90
   bracken:
@@ -74,6 +76,7 @@ run_modules:
   - nanoq
   - bowtie2
   - samtools
+  - hostile
   - kraken
   - kaiju
   - diamond
@@ -141,6 +144,8 @@ top_modules:
       name: "bowtie2"
   - "samtools":
       name: "Samtools Stats"
+  - "hostile":
+      name: "Hostile"
   - "kraken":
       name: "Kraken"
       path_filters: