From b914378c37aa59817cf2827ae58c94595636cf87 Mon Sep 17 00:00:00 2001
From: Kevin Lewis <kl2@sanger.ac.uk>
Date: Tue, 27 Aug 2024 16:10:24 +0100
Subject: [PATCH] add static parameter files for stage2 reanalysis

improve naming of template names and parameter names&values for stage2 input preprocessing
---
 .../stage2_reanalysis/align_bwa_mem2.json     | 13 +++++++
 .../base_params_duplexseq_cram.json           | 37 +++++++++++++++++++
 .../base_params_duplexseq_fastq.json          | 35 ++++++++++++++++++
 .../vtlib/alignment_wtsi_stage2_template.json |  3 +-
 ..._pi.json => stage2_preprocess_inputs.json} |  0
 5 files changed, 86 insertions(+), 2 deletions(-)
 create mode 100644 data/static_params/stage2_reanalysis/align_bwa_mem2.json
 create mode 100644 data/static_params/stage2_reanalysis/base_params_duplexseq_cram.json
 create mode 100644 data/static_params/stage2_reanalysis/base_params_duplexseq_fastq.json
 rename data/vtlib/{fastq_s2_pi.json => stage2_preprocess_inputs.json} (100%)

diff --git a/data/static_params/stage2_reanalysis/align_bwa_mem2.json b/data/static_params/stage2_reanalysis/align_bwa_mem2.json
new file mode 100644
index 00000000..477d9712
--- /dev/null
+++ b/data/static_params/stage2_reanalysis/align_bwa_mem2.json
@@ -0,0 +1,13 @@
+{
+  "assign": [
+    {
+      "alignment_method": "bwa_mem",
+      "bwa_executable": "bwa-mem2"
+    }
+  ],
+  "assign_local": {},
+  "ops": {
+    "splice": [],
+    "prune": []
+  }
+}
diff --git a/data/static_params/stage2_reanalysis/base_params_duplexseq_cram.json b/data/static_params/stage2_reanalysis/base_params_duplexseq_cram.json
new file mode 100644
index 00000000..bafe2753
--- /dev/null
+++ b/data/static_params/stage2_reanalysis/base_params_duplexseq_cram.json
@@ -0,0 +1,37 @@
+{
+  "assign": [
+    {
+      "spatial_filter_switch":"off",
+      "markdup_optical_distance_value": "100",
+      "s2_se_pe": "pe",
+      "samtools_executable": "samtools",
+      "s2_input_format": "cram",
+      "markdup_method": "duplexseq",
+      "s2_ppi_switch":"s2_ppi",
+      "pp_read2tags":"on",
+      "pp_import_method":"crammerge",
+      "fastq_s2_pi_fq1": "DUMMY",
+      "fastq_s2_pi_fq2": "DUMMY",
+      "fastq_s2_pi_RG_ID": "DUMMY",
+      "s2_filter_files": "DUMMY",
+      "spatial_filter_file": "DUMMY",
+      "phix_reference_genome_fasta":"DUMMY",
+      "realignment_switch":1
+    }
+  ],
+  "assign_local": {},
+  "ops": {
+    "splice": [
+      "aln_bam12auxmerge:-foptgt_000_fixmate:",
+      "foptgt_seqchksum_file:-scs_cmp_seqchksum:outputchk"
+    ],
+    "prune": [
+      "foptgt.*_bmd_multiway:calibration_pu-",
+      "foptgt_cram_tee:c2a-",
+      "foptgt.*samtools_stats_F0.*_target.*-",
+      "foptgt.*samtools_stats_F0.*00_bait.*-",
+      "aln_tee3_tee3:to_phix_aln-scs_cmp_seqchksum:outputchk",
+      "ssfqc_tee_ssfqc:subsample-"
+    ]
+  }
+}
diff --git a/data/static_params/stage2_reanalysis/base_params_duplexseq_fastq.json b/data/static_params/stage2_reanalysis/base_params_duplexseq_fastq.json
new file mode 100644
index 00000000..d5e42b8a
--- /dev/null
+++ b/data/static_params/stage2_reanalysis/base_params_duplexseq_fastq.json
@@ -0,0 +1,35 @@
+{
+  "assign": [
+    {
+      "spatial_filter_switch":"off",
+      "markdup_optical_distance_value": "100",
+      "s2_se_pe": "pe",
+      "samtools_executable": "samtools",
+      "s2_input_format": "cram",
+      "markdup_method": "duplexseq",
+      "s2_ppi_switch":"s2_ppi",
+      "pp_read2tags":"on",
+      "pp_import_method":"fastq",
+      "in_crams": "DUMMY",
+      "s2_filter_files": "DUMMY",
+      "spatial_filter_file": "DUMMY",
+      "phix_reference_genome_fasta":"DUMMY",
+      "realignment_switch":1
+    }
+  ],
+  "assign_local": {},
+  "ops": {
+    "splice": [
+      "aln_bam12auxmerge:-foptgt_000_fixmate:",
+      "foptgt_seqchksum_file:-scs_cmp_seqchksum:outputchk"
+    ],
+    "prune": [
+      "foptgt.*_bmd_multiway:calibration_pu-",
+      "foptgt_cram_tee:c2a-",
+      "foptgt.*samtools_stats_F0.*_target.*-",
+      "foptgt.*samtools_stats_F0.*00_bait.*-",
+      "aln_tee3_tee3:to_phix_aln-scs_cmp_seqchksum:outputchk",
+      "ssfqc_tee_ssfqc:subsample-"
+    ]
+  }
+}
diff --git a/data/vtlib/alignment_wtsi_stage2_template.json b/data/vtlib/alignment_wtsi_stage2_template.json
index 5d622004..bbb29e45 100644
--- a/data/vtlib/alignment_wtsi_stage2_template.json
+++ b/data/vtlib/alignment_wtsi_stage2_template.json
@@ -102,8 +102,7 @@
 				"select":"s2_ppi_switch", "default":"crammerge","select_range":[1],
 				"cases":{
 					"crammerge":"crammerge.json",
-					"pp_ns":"fastq_s2_pi.json",
-					"aviti":"elembio_nanoseq_s2_pi.json"
+					"s2_ppi":"stage2_preprocess_inputs.json"
 				}
 			}},
                 "subst_map":{"input_format":{"subst":"s2_input_format"}},
diff --git a/data/vtlib/fastq_s2_pi.json b/data/vtlib/stage2_preprocess_inputs.json
similarity index 100%
rename from data/vtlib/fastq_s2_pi.json
rename to data/vtlib/stage2_preprocess_inputs.json