refactor: remove sylph

.github/workflows/build_and_test.yml

@@ -38,21 +38,6 @@ jobs:
         run: |
           ln -s ~/kraken2_db_8 kraken2_db
 
-      - name: make sylph db # Needed so tests can run quickly
-        run: |
-          cd ~
-          if [ ! -d "gatekeeper_sylph_test_data" ]; then
-            mkdir gatekeeper_sylph_test_data
-            cp /mnt/portal-sp3dev-knowledge/sylph/gtdb-r220-c1000-dbv1.syldb gatekeeper_sylph_test_data
-            cp /mnt/portal-sp3dev-knowledge/sylph/virus_imgvr_c200_v0.3.0.syldb gatekeeper_sylph_test_data
-            cp /mnt/portal-sp3dev-knowledge/sylph/fungi-refseq-2024-07-25-c200-v0.3.syldb gatekeeper_sylph_test_data
-            cp /mnt/portal-sp3dev-knowledge/sylph/*.tsv* gatekeeper_sylph_test_data
-          fi
-
-      - name: symlink sylph db
-        run: |
-          ln -s ~/gatekeeper_sylph_test_data sylph_dbs
-
       # Run pytest in container to use conda environment
       - name: pytest in docker
         run: |

.gitignore

@@ -22,8 +22,6 @@ kraken2_db*
 results
 report*.html
 
-sylph_dbs
-
 # Python
 *__pycache__
 

CHANGELOG.md

@@ -1,8 +1,6 @@
 ## New
 
-- Code for generating sylph databases has been altered to incorporate ani_groups (based on taxid). This is only set for groups, not singletons
-- when making sylph databases the taxonomy tsv now have a header and gets the ani_group column
-- code for making virus sylph db now filters for human viruses
+- Remove Sylph
 
 ## 2.4.0
 

README.md

@@ -6,19 +6,16 @@ This pipeline should be used to perform check quality and trimming in sequence d
 * Nextflow (tested on version 23.04)
 * dependencies in [env.yml](env.yml)
 * Kraken2 [Standard dataset](https://benlangmead.github.io/aws-indexes/k2) (tested with Standard-8 from 2023/06/05).
-* For sylph: pre-built indexes and associated metadata.
 
 ## Running Pipeline ##
 Parameters:
 
 - **input_dir** = A directory containing input fastq.gz files
 - **seq_platform** = Sequencing platform `illumina` or `ont`
 - **kraken2_db_path** = Path to the kraken2 dataset
-- **workflow** = `sylph`, `flu`, or `myco`. `speciated` is deprecated.
+- **workflow** = `flu`, or `myco`. `speciated` is deprecated.
 - **mem_map** (Optional) = Use Kraken 2 memory mapping (requires preloading kraken2 db `cp -r <path_to_kraken2_db> /dev/shm`) `true` or `false`
 - **publish_dir** (Optional) If set will output files to directory provided.
-- **sylph_dbs** = Path to sylph database(s). See [here](https://github.com/bluenote-1577/sylph/wiki/Pre%E2%80%90built-databases)
-- **sylph_db_taxonomy_files** = Path taxonomy file(s) for sylph db. Should be tsv (optionally gzipped)
 
 See parameters with:
 ```bash
@@ -56,56 +53,6 @@ cp -r kraken_index /dev/shm/
 kraken2 --db /dev/shm/kraken_index --memory-mapping ...
 ```
 
-## Sylph
-
-Sylph is a k-mer based classification system that processes all the reads in one go, rather than classifying per read.
-It can accept multiple databases, so to incorporate fungi or viruses an extra database can be provided rather than needing to rebuild a single db.
-To use multiple databases it is easiest to set it in the `nextflow.config`:
-```bash
-params {
-  sylph_dbs = ["knowledge_bucket/sylph/refseq_bacteria_2025-08-04/refseq_bacteria_db_c200.syldb",
-              "knowledge_bucket/sylph/refseq_fungi_2025-08-04/refseq_fungi_db_c200.syldb",
-              "knowledge_bucket/sylph/refseq_viral_2025-08-04/refseq_viral_db_c100.syldb"]
-  sylph_db_taxonomy_files = ["knowledge_bucket/sylph/refseq_bacteria_2025-08-04/taxonomy.tsv.gz",
-                       "knowledge_bucket/sylph/refseq_fungi_2025-08-04/taxonomy.tsv.gz",
-                       "knowledge_bucket/sylph/refseq_viral_2025-08-04/taxonomy.tsv.gz"]
-}
-```
-
-The taxonomy file needs to fit the format required for [sylph-tax](https://sylph-docs.github.io/sylph-tax-custom-taxonomies/).
-As such it must be a two column TSV where the first column if the name of the fasta file, and the second column is the taxonomy string.
-From testing:
-- Can add a header without causing issues
-- Can add additional columns
-
-The taxonomy format for sylph-tax is the same as provided in the downloads from [GTDB](https://data.gtdb.aau.ecogenomic.org/releases/release226/226.0/)
-
-### Parameters
-There are two parameters used in the Sylph process:
-- `sylph_query_ani_threshold`: sets the minimum ani threshold from the query step. Sylph authors recommend 90.
-- `sylph_profile_ani_threshold`: sets the minimum ani threshold from the profile step. Sylph authors recommend 95.
-
-### Databases for use
-Preference is to go with NCBI over GTDB as it is more familiar to clinical users (Though GTDB likely works better).
-Likewise with viruses the focus should be on human pathogenic viruses rather than phages etc.
-
-In the knowledge bucket there are a variety of sylph databates.
-To use one in this pipeline requires the database itself plus a tsv with the taxonomy metadata.
-
-See [sylph_references](sylph_references/README.md) for details of creating databases from RefSeq (NCBI).
-
-Note: For database to be used in competitive mapping downstream it also requires a folder of the reference genomes to make a manifest from.
-As such the pre-built Sylph dbs are less useful except for GTDB which matches certain releases.
-
-### Data for tests
-Sylph tests expect a folder `sylph_dbs` containing the sylph [pre-built databases](https://github.com/bluenote-1577/sylph/wiki/Pre%E2%80%90built-databases) for testing.
-These are included in the knowledge bucket in the sylph directory. Specifically uses:
-- `gtdb-r220-c1000-dbv1.syldb` and `gtdb_r220_metadata.tsv.gz`
-- `virus_imgvr_c200_v0.3.0.syldb` and `virus_imgvr_4.1_metadata.tsv.gz`
-
-The c1000 means that the k-mers are sampled every 1000bp making it smaller than c200, and so useful for testing.
-The metadata/taxonomy file can be optionally gzipped.
-
 
 ## Development/Install
 The python side of this repo forms a python project.

env.yml

@@ -11,5 +11,3 @@ dependencies:
 - just=1.40.0
 - bracken=2.9
 - pytest=8.3.2
-- sylph=0.8.0
-- sylph-tax=1.1.2

main.nf

@@ -4,7 +4,6 @@ include { fastp } from './process/quality_check.nf'
 include { kraken2 ; summarise_taxa ; bracken_summarise_taxa } from './process/kraken2.nf'
 include { filter_myco ; filter_flu } from './process/filter_reads.nf'
 include { has_enough_reads } from './process/has_enough_reads.nf'
-include { sylph } from './process/sylph.nf'
 
 // Parameters
 params.input_paired_suffix = "*_{1,2}.fastq.gz"
@@ -15,8 +14,6 @@ params.gatekeeper_illumina_min_num_reads = 10000
 params.gatekeeper_ont_min_num_reads = 1000
 params.gatekeeper_confidence_threshold = 0.00
 params.gatekeeper_taxa_summary_threshold = 0.5
-params.sylph_query_ani_threshold = 90
-params.sylph_profile_ani_threshold = 95
 
 workflow {
     if (params.help) {
@@ -27,12 +24,10 @@ workflow {
 
             Parameters:
             ------------------------------------------------------------------------
-            --workflow    workflow to run: speciate, myco, sylph, speciate_detailed
+            --workflow    workflow to run: speciate, myco, speciate_detailed
             --input_dir    Path to directory containing input fastq files
             --seq_platform    sequencing platform: illumina or ont
             --kraken2_db_path   Path to the kraken dataset directory
-            --sylph_db    Path to the sylph database
-            --sylph_db_taxonomy    Path to the sylph database taxonomy metadata
 
             Optional:
             --mem_map    If 'true' use memory mapping for kraken2. See README for details
@@ -43,12 +38,12 @@ workflow {
     }
 
     if (params.seq_platform == 'ont') {
-        input_files = Channel.fromPath("${params.input_dir}/${params.input_single_suffix}", checkIfExists: true)
+        input_files = channel.fromPath("${params.input_dir}/${params.input_single_suffix}", checkIfExists: true)
             .ifEmpty { error("cannot find any reads matching ${params.input_single_suffix} in ${params.input_dir}") }
             .map { it -> tuple(it.simpleName, it) }
     }
     else if (params.seq_platform == 'illumina') {
-        input_files = Channel.fromFilePairs(
+        input_files = channel.fromFilePairs(
                 "${params.input_dir}/${params.input_paired_suffix}",
                 flat: false,
                 checkIfExists: true,
@@ -57,12 +52,12 @@ workflow {
             .ifEmpty { error("cannot find any reads matching ${params.input_paired_suffix} in ${params.input_dir}") }
     }
 
-    kraken2_db_path = Channel.fromPath(params.kraken2_db_path).first()
+    kraken2_db_path = channel.fromPath(params.kraken2_db_path).first()
 
     check_seq_platform(params.seq_platform, input_files)
 
     if (params.workflow == 'speciate') {
-        log.info("Speciate workflow is deprecated, consider sylph instead")
+        log.info("Speciate workflow is deprecated, consider sylph instead within competitive mapping")
         gatekeeper_speciate(input_files, kraken2_db_path, params.seq_platform)
     }
     else if (params.workflow == 'myco') {
@@ -71,9 +66,6 @@ workflow {
     else if (params.workflow == 'flu') {
         gatekeeper_flu(input_files, kraken2_db_path, params.seq_platform)
     }
-    else if (params.workflow == 'sylph') {
-        gatekeeper_sylph(input_files, params.sylph_dbs, params.sylph_db_taxonomy_files, params.seq_platform)
-    }
     else {
         error("Invalid workflow: ${params.workflow}")
     }
@@ -169,28 +161,6 @@ workflow gatekeeper_flu {
     gatekeeper_report = filter_flu.out.gatekeeper_report_json
 }
 
-workflow gatekeeper_sylph {
-    take:
-    fastq_files
-    sylph_dbs
-    sylph_db_taxonomy_files
-    seq_platform
-
-    main:
-    sylph(
-        fastq_files,
-        sylph_dbs,
-        sylph_db_taxonomy_files,
-        seq_platform,
-        params.sylph_query_ani_threshold,
-        params.sylph_profile_ani_threshold,
-    )
-
-    emit:
-    sylph_query = sylph.out.sylph_query
-    sylph_report = sylph.out.sylph_report
-    taxonomy_report = sylph.out.taxonomy_report
-}
 
 def check_seq_platform(seq_platform, fastq_files) {
     def seq_platforms = ['ont', 'illumina']

minimal_files.txt

@@ -7,5 +7,3 @@ process/templates/filter_myco.sh
 process/templates/filter_flu.sh
 process/templates/run_fastp.sh
 process/templates/run_kraken.sh
-process/sylph.nf
-process/templates/run_sylph.sh

pyproject.toml

@@ -55,5 +55,4 @@ version_files = [
     "process/kraken2.nf",
     "process/quality_check.nf",
     "process/filter_reads.nf",
-    "process/sylph.nf",
 ]