Fix hamronization fargene input

CHANGELOG.md

@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Breaking change`
 
-[#391](https://github.com/nf-core/funcscan/pull/391) Made all "database" parameter names consistent, skip hmmsearch by default. (by @jasmezz)
+- [#391](https://github.com/nf-core/funcscan/pull/391) Made all "database" parameter names consistent, skip hmmsearch by default. (by @jasmezz)
 
 | Old parameter                                    | New parameter                           |
 | ------------------------------------------------ | --------------------------------------- |
@@ -27,6 +27,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | `amp_skip_hmmsearch`                             | `amp_run_hmmsearch`                     |
 | `bgc_skip_hmmsearch`                             | `bgc_run_hmmsearch`                     |
 
+- [#343](https://github.com/nf-core/funcscan/pull/343) Standardized the resulting workflow summary tables to always start with 'sample_id\tcontig_id\t..'. Reformatted the output of `hamronization/summarize` module. (by @darcy220606)
+- [#411](https://github.com/nf-core/funcscan/pull/411) Optimised hAMRonization input: only high-quality hits from fARGene output are reported. (by @jasmezz, @jfy133)
+
 ### `Added`
 
 - [#322](https://github.com/nf-core/funcscan/pull/322) Updated all modules: introduce environment.yml files. (by @jasmezz)
@@ -44,7 +47,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#343](https://github.com/nf-core/funcscan/pull/343) Standardized the resulting workflow summary tables to always start with 'sample_id\tcontig_id\t..'. Reformatted the output of `hamronization/summarize` module. (by @darcy220606)
 - [#348](https://github.com/nf-core/funcscan/pull/348) Updated samplesheet for pipeline tests to 'samplesheet_reduced.csv' with smaller datasets to reduce resource consumption. Updated prodigal module to fix pigz issue. Removed `tests/` from `.gitignore`. (by @darcy220606)
 - [#362](https://github.com/nf-core/funcscan/pull/362) Save annotations from bakta in subdirectories per sample. (by @jasmezz)
 - [#363](https://github.com/nf-core/funcscan/pull/363) Removed warning from DeepBGC usage docs. (by @jasmezz)
@@ -53,7 +55,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#376](https://github.com/nf-core/funcscan/pull/376) Fixed an occasional RGI process failure when certain files not produced. (❤️ to @amizeranschi for reporting, fix by @amizeranschi & @jfy133)
 - [#386](https://github.com/nf-core/funcscan/pull/386) Updated DeepBGC module to fix output file names, separate annotation step for all BGC tools, add warning if no BGCs found, fix MultiQC reporting of annotation workflow. (by @jfy133, @jasmezz)
 - [#392](https://github.com/nf-core/funcscan/pull/392) & [#397](https://github.com/nf-core/funcscan/pull/397) Fixed a docker/singularity only error appearing when running with conda. (❤️ to @ewissel for reporting, fix by @jfy33 & @jasmezz)
-- [#394](https://github.com/nf-core/funcscan/pull/394) Fixed BGC input channel: pre-annotated input is picked up correctly now. (by @jfy133, @jasmezz)
 - [#391](https://github.com/nf-core/funcscan/pull/391) Skip hmmmsearch by default to not crash pipeline if user provides no HMM files, updated docs. (by @jasmezz)
 - [#397](https://github.com/nf-core/funcscan/pull/397) Removed deprecated AMPcombi module, fixed variable name in BGC workflow, updated minor parts in docs (usage, parameter schema). (by @jasmezz)
 - [#402](https://github.com/nf-core/funcscan/pull/402) Fixed BGC length calculation for antiSMASH hits by comBGC. (by @jasmezz)

conf/modules.config

@@ -279,13 +279,13 @@ process {
                 path: { "${params.outdir}/arg/fargene/${meta.id}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                pattern: "*/{predictedGenes,retrievedFragments}/*"
+                pattern: "*/{hmmsearchresults,predictedGenes,retrievedFragments}/*"
             ],
             [
                 path: { "${params.outdir}/arg/fargene/${meta.id}/" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                pattern: "*/{hmmsearchresults,tmpdir}/*",
+                pattern: "*/{tmpdir}/*",
                 enabled: params.arg_fargene_savetmpfiles
             ]
         ]

docs/output.md

@@ -327,7 +327,7 @@ Output Summaries:
 - `fargene/`
   - `fargene_analysis.log`: logging output that fARGene produced during its run
   - `<sample_name>/`:
-    - `hmmsearchresults/`: output from intermediate hmmsearch step (only if `--arg_fargene_savetmpfiles` supplied)
+    - `hmmsearchresults/`: output from intermediate hmmsearch step
     - `predictedGenes/`:
       - `*-filtered.fasta`: nucleotide sequences of predicted ARGs
       - `*-filtered-peptides.fasta`: amino acid sequences of predicted ARGs

modules.json

@@ -55,6 +55,11 @@
                         "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
+                    "argnorm": {
+                        "branch": "master",
+                        "git_sha": "e4fc46af5ec30070e6aef780aba14f89a28caa88",
+                        "installed_by": ["modules"]
+                    },
                     "bakta/bakta": {
                         "branch": "master",
                         "git_sha": "9d0f89b445e1f5b2fb30476f4be9a8b519c07846",
@@ -87,7 +92,7 @@
                     },
                     "fargene": {
                         "branch": "master",
-                        "git_sha": "a7231cbccb86535529e33859e05d19ac93f3ea04",
+                        "git_sha": "9cf6f5e4ad9cc11a670a94d56021f1c4f9a91ec1",
                         "installed_by": ["modules"]
                     },
                     "gecco/run": {
@@ -205,11 +210,6 @@
                         "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/untar/untar.diff"
-                    },
-                    "argnorm": {
-                        "branch": "master",
-                        "git_sha": "e4fc46af5ec30070e6aef780aba14f89a28caa88",
-                        "installed_by": ["modules"]
                     }
                 }
             },