From 964f5d01c097177cafddab9666770c462fb94ba4 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 8 Aug 2024 16:04:20 +1000
Subject: [PATCH 01/22] feat(conf/dbs): Added variables for database names, and
 file names

---
 conf/dbs.config | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/conf/dbs.config b/conf/dbs.config
index 4b2d0e4f..78863ffb 100644
--- a/conf/dbs.config
+++ b/conf/dbs.config
@@ -21,6 +21,28 @@ params {
     pdb_seqres        = 'ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt'
     uniprot_sprot     = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz'
     uniprot_trembl    = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz'
+    
+    def bfd_name           = params.bfd ?: 'bfd'
+    def smallbfd_name      = params.smallbfd ?: 'smallbfd'
+    def mgnify_name        = params.mgnify ?: 'mgnify'
+    def pdb70_name         = params.pdb70 ?: 'pdb70'
+    def pdb_mmcif_name     = params.pdb_mmcif ?: 'pdb_mmcif'
+    def uniclust30_name    = params.uniclust30 ?: 'uniclust30'
+    def uniref90_name      = params.uniref90 ?: 'uniref90'
+    def pdb_seqres_name    = params.pdb_seq ?: 'pdb_seqres'
+    def uniprot_name       = params.uniprot ?: 'uniprot'
+    def alphafold_params_name = params.alphafold_params ?: 'alphafold_params_*'
+    def mmcif_files_name   = params.mmcif_path ?: 'pdb_mmcif/mmcif_files/'
+    def mmcif_obsolete_name = params.mmcif_obsolete ?: 'pdb_mmcif/obsolete.dat'
+
+    def uniclust30_db_name = params.uniclust30_db ?: 'uniclust30_2018_08'
+    def bfd_first_non_consensus_sequences_name = params.bfd_first_non_consensus_sequences ?: 'bfd-first_non_consensus_sequences.fasta' 
+    def uniprot_fasta_name = params.uniprot_fasta ?: 'uniprot.fasta'
+    def pdb_seqres_txt_name = params.pdb_seqres_txt ?: 'pdb_seqres.txt'
+    def bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name = params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt ?: 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt'
+    def uniref90_fasta_name = params.uniref90_fasta ?: 'uniref90.fasta'
+    def mgy_clusters_fasta_name = params.mgy_clusters_fasta ?: 'mgy_clusters_2022_05.fa'
+    
 
     // Alphafold paths
     bfd_path               = "${params.alphafold2_db}/bfd/*"

From 2a79fe43af25a20a77eb3b3505075794eeea5efb Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 8 Aug 2024 16:05:27 +1000
Subject: [PATCH 02/22] feat(conf/dbs): Changed config paths to use database
 variables instead of hardcoded values

---
 conf/dbs.config | 57 ++++++++++++++++++++++++++++++-------------------
 1 file changed, 35 insertions(+), 22 deletions(-)

diff --git a/conf/dbs.config b/conf/dbs.config
index 78863ffb..8f061a7e 100644
--- a/conf/dbs.config
+++ b/conf/dbs.config
@@ -45,35 +45,48 @@ params {
     
 
     // Alphafold paths
-    bfd_path               = "${params.alphafold2_db}/bfd/*"
-    small_bfd_path         = "${params.alphafold2_db}/small_bfd/*"
+    bfd_path               = "${params.alphafold2_db}/${bfd_name}/*"
+    small_bfd_path         = "${params.alphafold2_db}/${small_bfd_name}/*"
     //alphafold2_params_path = "${params.alphafold2_db}/alphafold_params_*/*"
-    alphafold2_params_path = "${params.alphafold2_db}/params/*"
-    mgnify_path            = "${params.alphafold2_db}/mgnify/*"
-    pdb70_path             = "${params.alphafold2_db}/pdb70/**"
-    pdb_mmcif_path         = "${params.alphafold2_db}/pdb_mmcif/**"
+    //alphafold2_params_path = "${params.alphafold2_db}/params/*"
+    alphafold2_params_path = "${params.alphafold2_db}/${alphafold_params_name}/*"
+    mgnify_path            = "${params.alphafold2_db}/${mgnify_name}/*"
+    pdb70_path             = "${params.alphafold2_db}/${pdb70_name}/**"
+    pdb_mmcif_path         = "${params.alphafold2_db}/${pdb_mmcif_name}/**"
     //uniclust30_path        = "${params.alphafold2_db}/uniclust30/**"
-    uniclust30_path        = "/srv/scratch/sbf/uniclust30/**"
-    uniref90_path          = "${params.alphafold2_db}/uniref90/*"
-    pdb_seqres_path        = "${params.alphafold2_db}/pdb_seqres/*"
-    uniprot_path           = "${params.alphafold2_db}/uniprot/*"
+    //uniclust30_path        = "/srv/scratch/sbf/uniclust30/**"
+    uniclust30_path        = "${params.alphafold2_db}/${uniclust30_name}/**"
+    uniref90_path          = "${params.alphafold2_db}/${uniref90_name}/*"
+    pdb_seqres_path        = "${params.alphafold2_db}/${pdb_seqres_name}/*"
+    uniprot_path           = "${params.alphafold2_db}/${uniprot_name}/*"
 
     // Alphafold variables
-    bfd_variable               = "${params.alphafold2_db}/bfd/"
-    small_bfd_variable         = "${params.alphafold2_db}/smallbfd/"
-    mgnify_variable            = "${params.alphafold2_db}/mgnify/"
-    pdb70_variable             = "${params.alphafold2_db}/pdb70/"
-    pdb_mmcif_variable         = "${params.alphafold2_db}/pdb_mmcif/"
+    //bfd_variable               = "${params.alphafold2_db}/bfd/"
+    bfd_dir_path               = "${params.alpahfold2_db}/${bfd_name}/"
+    //small_bfd_variable         = "${params.alphafold2_db}/smallbfd/"
+    small_bfd_dir_path         = "${params.alphafold2_db}/${smallbfd_name}/"
+    //mgnify_variable            = "${params.alphafold2_db}/mgnify/"
+    mgnify_dir_path            = "${params.alphafold2_db}/${mgnify_name}/"
+    //pdb70_variable             = "${params.alphafold2_db}/pdb70/"
+    pdb70_dir_path             = "${params.alphafold2_db}/${pdb70_name}/"
+    //pdb_mmcif_variable         = "${params.alphafold2_db}/pdb_mmcif/"
+    pdb_mmcif_dir_path         = "${params.alphafold2_db}/${pdb_mmcif_name}/"
     //uniclust30_variable        = "${params.alphafold2_db}/uniclust30/"
-    uniclust30_variable        = "/srv/scratch/sbf/uniclust30/"
-    uniref90_variable          = "${params.alphafold2_db}/uniref90/"
-    pdb_seqres_variable        = "${params.alphafold2_db}/pdb_seqres/"
-    uniprot_variable           = "${params.alphafold2_db}/uniprot/"
+    //uniclust30_variable        = "/srv/scratch/sbf/uniclust30/"
+    uniclust30_dir_path        = "${params.alphafold2_db}/${uniclust30_name}/"
+    //uniref90_variable          = "${params.alphafold2_db}/uniref90/"
+    uniref90_dir_path          = "${params.alpahfold2_db}/${uniref90_name}/"
+    //pdb_seqres_variable        = "${params.alphafold2_db}/pdb_seqres/"
+    pdb_seqres_dir_path        = "${params.alphafold2_db}/${pdb_seqres_name}/"
+    //uniprot_variable           = "${params.alphafold2_db}/uniprot/"
+    uniprot_dir_path           = "${params.alphafold2_db}/${uniprot_name}/"
 
     // Alphafold MSA Variables
-    mgnify_database_path       = "${params.alphafold2_db}/mgnify/"
-    template_mmcif_dir         = "${params.alphafold2_db}/pdb_mmcif/mmcif_files/"
-    obsolete_pdbs_path         = "${params.alphafold2_db}/pdb_mmcif/obsolete.dat"
+    mgnify_database_path       = "${params.alphafold2_db}/${mgnify_name}/"
+    //template_mmcif_dir         = "${params.alphafold2_db}/pdb_mmcif/mmcif_files/"
+    template_mmcif_dir         = "${params.alphafold2_db}/${mmcif_files_name}/"
+    //obsolete_pdbs_path         = "${params.alphafold2_db}/pdb_mmcif/obsolete.dat"
+    obsolete_pdbs_path         = "${params.alphafold2_db}/${mmcif_obsolete_name}"
 
     // Colabfold links
     colabfold_db_link = 'http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz'

From c218ad261b2b1d3d0abadfc84002d5dee3ddb829 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 8 Aug 2024 16:06:46 +1000
Subject: [PATCH 03/22] feat(run_alphafold2): Changed hardcoded paths to use
 variables and updated variable names

---
 modules/local/run_alphafold2.nf | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf
index 731ad1c1..5cf964dd 100644
--- a/modules/local/run_alphafold2.nf
+++ b/modules/local/run_alphafold2.nf
@@ -34,28 +34,30 @@ process RUN_ALPHAFOLD2 {
 
     script:
     def args = task.ext.args ?: ''
-    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_variable}bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniclust30_database_path=${params.uniclust30_variable}uniclust30_2018_08/uniclust30_2018_08" :
-        "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}bfd-first_non_consensus_sequences.fasta"
+    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_dir_path}${params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name} --uniclust30_database_path=${params.uniclust30_dir_path}${params.uniclust30_db_name}" :
+        "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}${params.bfd_first_non_consensus_sequences_name}"
     if (alphafold2_model_preset == 'multimer') {
-        alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_variable}pdb_seqres.txt --uniprot_database_path=${params.uniprot_variable}uniprot.fasta "
+        alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} --uniprot_database_path=${params.uniprot_dir_path}${params.uniprot_fasta_name} "
     }
     else {
-        alphafold2_model_preset += " --pdb70_database_path=${params.pdb70_variable}pdb70 "
+        alphafold2_model_preset += " --pdb70_database_path=${params.pdb_dir_path}${params.pdb70_name} "
     }
     """
-    if [ -f ${params.pdb_seqres_variable}pdb_seqres.txt ]
-        then sed -i "/^\\w*0/d" ${params.pdb_seqres_variable}pdb_seqres.txt
+    if [ -f ${params.pdb_seqres_dir_path}/${params.pbd_seqres_txt_name} ]
+        \$PDB_SEQRES_TEMP=\$(mktemp --directory)
+        cp ${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} \${PDB_SEQRES_TEMP}/
+        then sed -i "/^\\w*0/d" \$PDB_SEQERS_TEMP/${params.pdb_seqres_txt_name}
     fi
-    if [ -d params/alphafold_params_* ]; then ln -r -s params/alphafold_params_*/* params/; fi
+    if [ -d ${params.alphafold2_params_path} ]; then ln -r -s ${params.alphafold2_params_path} params/; fi
     python3 /app/alphafold/run_alphafold.py \
         --fasta_paths=${fasta} \
         --model_preset=${alphafold2_model_preset} \
         --db_preset=${db_preset} \
         --output_dir=\$PWD \
         --data_dir=\$PWD \
-        --uniref90_database_path=${params.uniref90_variable}uniref90.fasta \
-        --template_mmcif_dir=${params.pdb_mmcif_variable}mmcif_files \
-        --obsolete_pdbs_path=${params.pdb_mmcif_variable}obsolete.dat \
+        --uniref90_database_path=${params.uniref90_dir_path}uniref90.fasta \
+        --template_mmcif_dir=${params.template_mmcif_dir} \
+        --obsolete_pdbs_path=${params.obsolete_pdbs_path} \
         --random_seed=53343 \
         $args
 

From edff052c835dbd439e16432e0a2ae1ec3b08221d Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 8 Aug 2024 16:07:42 +1000
Subject: [PATCH 04/22] feat(run_alphafold2_msa): Removed hardcoded paths and
 changed variables

---
 modules/local/run_alphafold2_msa.nf | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf
index 10d217ca..2e2bbe9b 100644
--- a/modules/local/run_alphafold2_msa.nf
+++ b/modules/local/run_alphafold2_msa.nf
@@ -35,13 +35,13 @@ process RUN_ALPHAFOLD2_MSA {
 
     script:
     def args = task.ext.args ?: ''
-    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_variable}bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniclust30_database_path=${params.uniclust30_variable}uniclust30_2018_08" :
-        "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}bfd-first_non_consensus_sequences.fasta"
+    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_dir_path}${params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name} --uniclust30_database_path=${params.uniclust30_dir_path}${uniclust30_db_name}" :
+        "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}${params.bfd_first_non_consensus_sequences_name}"
     if (alphafold2_model_preset == 'multimer') {
-        alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_variable}pdb_seqres.txt --uniprot_database_path=${params.uniprot_variable}/uniprot.fasta "
+        alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} --uniprot_database_path=${params.uniprot_dir_path}/${params.uniprot_fasta_name} "
     }
     else {
-        alphafold2_model_preset += " --pdb70_database_path=${params.pdb70_variable}pdb70 "
+        alphafold2_model_preset += " --pdb70_database_path=${params.pdb70_dir_path}${params.pdb70_name} "
     }
     """
     #if [ -f pdb_seqres/pdb_seqres.txt ]
@@ -55,8 +55,8 @@ process RUN_ALPHAFOLD2_MSA {
         --db_preset=${db_preset} \
         --output_dir=\$PWD \
         --data_dir=\$PWD \
-        --uniref90_database_path=${params.uniref90_variable}uniref90.fasta \
-        --mgnify_database_path=${params.mgnify_database_path}/mgy_clusters_2022_05.fa \
+        --uniref90_database_path=${params.uniref90_dir_path}/${params.uniref90_fasta_name} \
+        --mgnify_database_path=${params.mgnify_database_path}/${params.mgy_clusters_fasta_name} \
         --template_mmcif_dir=${params.template_mmcif_dir} \
         --obsolete_pdbs_path=${params.obsolete_pdbs_path}  \
         $args

From ea4459a713655395514c5db9897554e457d75dfc Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 8 Aug 2024 16:08:19 +1000
Subject: [PATCH 05/22] feat(run_alphafold2_msa): Added code from
 run_alphafold2.nf so that the script does not attempt to modify the existing
 database file

---
 modules/local/run_alphafold2_msa.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf
index 2e2bbe9b..ac3bd143 100644
--- a/modules/local/run_alphafold2_msa.nf
+++ b/modules/local/run_alphafold2_msa.nf
@@ -44,10 +44,10 @@ process RUN_ALPHAFOLD2_MSA {
         alphafold2_model_preset += " --pdb70_database_path=${params.pdb70_dir_path}${params.pdb70_name} "
     }
     """
-    #if [ -f pdb_seqres/pdb_seqres.txt ]
+    #if [ -f ${params.pdb_seqres_dir_path}/${params.pbd_seqres_txt_name} ]
     #    \$PDB_SEQRES_TEMP=\$(mktemp --directory)
-    #    cp ${params.pdb_seqres_variable}pdb_seqres.txt \${PDB_SEQRES_TEMP}/
-    #    then sed -i "/^\\w*0/d" \$PDB_SEQERS_TEMP/pdb_seqres.txt
+    #    cp ${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} \${PDB_SEQRES_TEMP}/
+    #    then sed -i "/^\\w*0/d" \$PDB_SEQERS_TEMP/${params.pdb_seqres_txt_name}
     #fi
     python3 /app/alphafold/run_msa.py \
         --fasta_paths=${fasta} \

From 83ca302ab2222552c07dd5c834c3c5c86808ccb3 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 9 Aug 2024 09:28:30 +1000
Subject: [PATCH 06/22] fix(conf/dbs): Changed variable names to have _prefix
 on the end to avoid conflicts with existing link variables

---
 conf/dbs.config | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/conf/dbs.config b/conf/dbs.config
index 8f061a7e..03c06b37 100644
--- a/conf/dbs.config
+++ b/conf/dbs.config
@@ -22,16 +22,16 @@ params {
     uniprot_sprot     = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz'
     uniprot_trembl    = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz'
     
-    def bfd_name           = params.bfd ?: 'bfd'
-    def smallbfd_name      = params.smallbfd ?: 'smallbfd'
-    def mgnify_name        = params.mgnify ?: 'mgnify'
-    def pdb70_name         = params.pdb70 ?: 'pdb70'
-    def pdb_mmcif_name     = params.pdb_mmcif ?: 'pdb_mmcif'
-    def uniclust30_name    = params.uniclust30 ?: 'uniclust30'
-    def uniref90_name      = params.uniref90 ?: 'uniref90'
-    def pdb_seqres_name    = params.pdb_seq ?: 'pdb_seqres'
-    def uniprot_name       = params.uniprot ?: 'uniprot'
-    def alphafold_params_name = params.alphafold_params ?: 'alphafold_params_*'
+    def bfd_name           = params.bfd_prefix ?: 'bfd'
+    def smallbfd_name      = params.smallbfd_prefix ?: 'smallbfd'
+    def mgnify_name        = params.mgnify_prefix ?: 'mgnify'
+    def pdb70_name         = params.pdb70_prefix ?: 'pdb70'
+    def pdb_mmcif_name     = params.pdb_mmcif_prefix ?: 'pdb_mmcif'
+    def uniclust30_name    = params.uniclust30_prefix ?: 'uniclust30'
+    def uniref90_name      = params.uniref90_prefix ?: 'uniref90'
+    def pdb_seqres_name    = params.pdb_seq_prefix ?: 'pdb_seqres'
+    def uniprot_name       = params.uniprot_prefix ?: 'uniprot'
+    def alphafold_params_name = params.alphafold_params_prefix ?: 'alphafold_params_*'
     def mmcif_files_name   = params.mmcif_path ?: 'pdb_mmcif/mmcif_files/'
     def mmcif_obsolete_name = params.mmcif_obsolete ?: 'pdb_mmcif/obsolete.dat'
 

From faba0abfd77997cfc168a5203db2b98b0abe4df9 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 9 Aug 2024 09:29:18 +1000
Subject: [PATCH 07/22] fix(conf/dbs): Changed existing variables to use new
 prefix variables

---
 conf/dbs.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/dbs.config b/conf/dbs.config
index 03c06b37..257b7d18 100644
--- a/conf/dbs.config
+++ b/conf/dbs.config
@@ -46,7 +46,7 @@ params {
 
     // Alphafold paths
     bfd_path               = "${params.alphafold2_db}/${bfd_name}/*"
-    small_bfd_path         = "${params.alphafold2_db}/${small_bfd_name}/*"
+    small_bfd_path         = "${params.alphafold2_db}/${smallbfd_name}/*"
     //alphafold2_params_path = "${params.alphafold2_db}/alphafold_params_*/*"
     //alphafold2_params_path = "${params.alphafold2_db}/params/*"
     alphafold2_params_path = "${params.alphafold2_db}/${alphafold_params_name}/*"
@@ -62,7 +62,7 @@ params {
 
     // Alphafold variables
     //bfd_variable               = "${params.alphafold2_db}/bfd/"
-    bfd_dir_path               = "${params.alpahfold2_db}/${bfd_name}/"
+    bfd_dir_path               = "${params.alphafold2_db}/${bfd_name}/"
     //small_bfd_variable         = "${params.alphafold2_db}/smallbfd/"
     small_bfd_dir_path         = "${params.alphafold2_db}/${smallbfd_name}/"
     //mgnify_variable            = "${params.alphafold2_db}/mgnify/"
@@ -75,7 +75,7 @@ params {
     //uniclust30_variable        = "/srv/scratch/sbf/uniclust30/"
     uniclust30_dir_path        = "${params.alphafold2_db}/${uniclust30_name}/"
     //uniref90_variable          = "${params.alphafold2_db}/uniref90/"
-    uniref90_dir_path          = "${params.alpahfold2_db}/${uniref90_name}/"
+    uniref90_dir_path          = "${params.alphafold2_db}/${uniref90_name}/"
     //pdb_seqres_variable        = "${params.alphafold2_db}/pdb_seqres/"
     pdb_seqres_dir_path        = "${params.alphafold2_db}/${pdb_seqres_name}/"
     //uniprot_variable           = "${params.alphafold2_db}/uniprot/"

From 04cad9dcd24256d3e5866857049826b7096540b8 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 9 Aug 2024 09:34:32 +1000
Subject: [PATCH 08/22] feat(nextflow.config): Added new param variables and
 defaults to the config file

---
 nextflow.config | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index ec71afb5..691ee289 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,6 +20,48 @@ params {
     full_dbs                    =  false // true full_dbs, false reduced_dbs
     alphafold2_model_preset     = "monomer" // for AF2 {monomer (default), monomer_casp14, monomer_ptm, multimer}
     alphafold2_db               = null
+    
+    // Database prefixes
+    bfd_prefix			= null
+    smallbfd_prefix		= null
+    mgnify_prefix		= null
+    pdb70_prefix		= null
+    pdb_mmcif_prefix		= null
+    uniclust30_prefix		= null
+    uniref90_prefix		= null
+    pdb_seq_prefix		= null
+    uniprot_prefix		= null
+    alphafold_params_prefix	= null
+    mmcif_path			= null
+    mmcif_obsolete		= null
+    uniclust30_db		= null
+    bfd_first_non_consensus_sequences = null
+    uniprot_fasta		= null
+    pdb_seqres_txt		= null
+    bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt = null
+    uniref90_fasta		= null
+    mgy_clusters_fasta		= null
+    uniclust30_prefix		= null
+
+    bfd_name			= null
+    smallbfd_name		= null
+    mgnify_name			= null
+    pdb70_name			= null
+    pdb_mmcif_name		= null
+    uniclust30_name		= null
+    uniref90_name		= null
+    pdb_seqres_name		= null
+    uniprot_name		= null
+    alphafold_params_name	= null
+    mmcif_files_name		= null
+    mmcif_obsolete_name		= null
+    uniclust30_db_name		= null
+    bfd_first_non_consensus_sequences_name = null
+    uniprot_fasta_name		= null
+    pdb_seqres_txt_name		= null
+    bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name = null
+    uniref90_fasta_name		= null
+    mgy_clusters_fasta_name	= null
 
     // Alphafold2 links
     bfd                         = null

From afeb1226dd023a6c199976aacd94694c6a033957 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 9 Aug 2024 12:38:11 +1000
Subject: [PATCH 09/22] feat(dbs): Made variables global

---
 conf/dbs.config | 38 +++++++++++++++++++-------------------
 1 file changed, 19 insertions(+), 19 deletions(-)

diff --git a/conf/dbs.config b/conf/dbs.config
index 257b7d18..5c34c852 100644
--- a/conf/dbs.config
+++ b/conf/dbs.config
@@ -22,26 +22,26 @@ params {
     uniprot_sprot     = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz'
     uniprot_trembl    = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz'
     
-    def bfd_name           = params.bfd_prefix ?: 'bfd'
-    def smallbfd_name      = params.smallbfd_prefix ?: 'smallbfd'
-    def mgnify_name        = params.mgnify_prefix ?: 'mgnify'
-    def pdb70_name         = params.pdb70_prefix ?: 'pdb70'
-    def pdb_mmcif_name     = params.pdb_mmcif_prefix ?: 'pdb_mmcif'
-    def uniclust30_name    = params.uniclust30_prefix ?: 'uniclust30'
-    def uniref90_name      = params.uniref90_prefix ?: 'uniref90'
-    def pdb_seqres_name    = params.pdb_seq_prefix ?: 'pdb_seqres'
-    def uniprot_name       = params.uniprot_prefix ?: 'uniprot'
-    def alphafold_params_name = params.alphafold_params_prefix ?: 'alphafold_params_*'
-    def mmcif_files_name   = params.mmcif_path ?: 'pdb_mmcif/mmcif_files/'
-    def mmcif_obsolete_name = params.mmcif_obsolete ?: 'pdb_mmcif/obsolete.dat'
+    bfd_name           = params.bfd_prefix ?: 'bfd'
+    smallbfd_name      = params.smallbfd_prefix ?: 'smallbfd'
+    mgnify_name        = params.mgnify_prefix ?: 'mgnify'
+    pdb70_name         = params.pdb70_prefix ?: 'pdb70'
+    pdb_mmcif_name     = params.pdb_mmcif_prefix ?: 'pdb_mmcif'
+    uniclust30_name    = params.uniclust30_prefix ?: 'uniclust30'
+    uniref90_name      = params.uniref90_prefix ?: 'uniref90'
+    pdb_seqres_name    = params.pdb_seq_prefix ?: 'pdb_seqres'
+    uniprot_name       = params.uniprot_prefix ?: 'uniprot'
+    alphafold_params_name = params.alphafold_params_prefix ?: 'alphafold_params_*'
+    mmcif_files_name   = params.mmcif_path ?: 'pdb_mmcif/mmcif_files/'
+    mmcif_obsolete_name = params.mmcif_obsolete ?: 'pdb_mmcif/obsolete.dat'
 
-    def uniclust30_db_name = params.uniclust30_db ?: 'uniclust30_2018_08'
-    def bfd_first_non_consensus_sequences_name = params.bfd_first_non_consensus_sequences ?: 'bfd-first_non_consensus_sequences.fasta' 
-    def uniprot_fasta_name = params.uniprot_fasta ?: 'uniprot.fasta'
-    def pdb_seqres_txt_name = params.pdb_seqres_txt ?: 'pdb_seqres.txt'
-    def bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name = params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt ?: 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt'
-    def uniref90_fasta_name = params.uniref90_fasta ?: 'uniref90.fasta'
-    def mgy_clusters_fasta_name = params.mgy_clusters_fasta ?: 'mgy_clusters_2022_05.fa'
+    uniclust30_db_name = params.uniclust30_db ?: 'uniclust30_2018_08'
+    bfd_first_non_consensus_sequences_name = params.bfd_first_non_consensus_sequences ?: 'bfd-first_non_consensus_sequences.fasta' 
+    uniprot_fasta_name = params.uniprot_fasta ?: 'uniprot.fasta'
+    pdb_seqres_txt_name = params.pdb_seqres_txt ?: 'pdb_seqres.txt'
+    bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name = params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt ?: 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt'
+    uniref90_fasta_name = params.uniref90_fasta ?: 'uniref90.fasta'
+    mgy_clusters_fasta_name = params.mgy_clusters_fasta ?: 'mgy_clusters_2022_05.fa'
     
 
     // Alphafold paths

From 3d615b75f76cb6d2bc8dcc991e0378d47f748e79 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:19:28 +1000
Subject: [PATCH 10/22] fix(dbs): Changed database directory default

---
 conf/dbs.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/dbs.config b/conf/dbs.config
index 5c34c852..7d06e41a 100644
--- a/conf/dbs.config
+++ b/conf/dbs.config
@@ -31,7 +31,7 @@ params {
     uniref90_name      = params.uniref90_prefix ?: 'uniref90'
     pdb_seqres_name    = params.pdb_seq_prefix ?: 'pdb_seqres'
     uniprot_name       = params.uniprot_prefix ?: 'uniprot'
-    alphafold_params_name = params.alphafold_params_prefix ?: 'alphafold_params_*'
+    alphafold_params_name = params.alphafold_params_prefix ?: 'params/alphafold_params_*'
     mmcif_files_name   = params.mmcif_path ?: 'pdb_mmcif/mmcif_files/'
     mmcif_obsolete_name = params.mmcif_obsolete ?: 'pdb_mmcif/obsolete.dat'
 

From cb292568f827613e116316a30893741e1e02b36e Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:20:37 +1000
Subject: [PATCH 11/22] feat(katana): Temporarily removed PBS job scheduling

---
 conf/katana.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/katana.config b/conf/katana.config
index a344ffc0..67f310a7 100644
--- a/conf/katana.config
+++ b/conf/katana.config
@@ -19,7 +19,7 @@ process {
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
-    executor = 'pbspro'
+    //executor = 'pbspro'
 
     errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
     maxRetries    = 1

From 5829301a5cc29d5b2d5b09b8b53e4ca05c975de6 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:22:29 +1000
Subject: [PATCH 12/22] fix(run_alphafold2): Fixed copy command to point to the
 correct directory

---
 modules/local/run_alphafold2.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf
index 5cf964dd..30163279 100644
--- a/modules/local/run_alphafold2.nf
+++ b/modules/local/run_alphafold2.nf
@@ -43,7 +43,7 @@ process RUN_ALPHAFOLD2 {
         alphafold2_model_preset += " --pdb70_database_path=${params.pdb_dir_path}${params.pdb70_name} "
     }
     """
-    if [ -f ${params.pdb_seqres_dir_path}/${params.pbd_seqres_txt_name} ]
+    if [ -f ${params.pdb_seqres_dir_path}/${params.pdb_seqres_txt_name} ]
         \$PDB_SEQRES_TEMP=\$(mktemp --directory)
         cp ${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} \${PDB_SEQRES_TEMP}/
         then sed -i "/^\\w*0/d" \$PDB_SEQERS_TEMP/${params.pdb_seqres_txt_name}

From 485e400f5198b94bff46f0a90b784d4f1fbddf7b Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:23:33 +1000
Subject: [PATCH 13/22] fix(run_alphafold2): Updated paths to point to the
 correct uniclust databse

---
 modules/local/run_alphafold2_msa.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf
index ac3bd143..89667a73 100644
--- a/modules/local/run_alphafold2_msa.nf
+++ b/modules/local/run_alphafold2_msa.nf
@@ -35,7 +35,7 @@ process RUN_ALPHAFOLD2_MSA {
 
     script:
     def args = task.ext.args ?: ''
-    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_dir_path}${params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name} --uniclust30_database_path=${params.uniclust30_dir_path}${uniclust30_db_name}" :
+    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_dir_path}${params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name} --uniclust30_database_path=${params.uniclust30_dir_path}${params.uniclust30_db_name}" :
         "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}${params.bfd_first_non_consensus_sequences_name}"
     if (alphafold2_model_preset == 'multimer') {
         alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} --uniprot_database_path=${params.uniprot_dir_path}/${params.uniprot_fasta_name} "

From d008f38feec0e74c8704f252c84883059eb53437 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:26:32 +1000
Subject: [PATCH 14/22] fix(run_alphafold2): Fixed typo

---
 modules/local/run_alphafold2_msa.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf
index 89667a73..d4fa4f53 100644
--- a/modules/local/run_alphafold2_msa.nf
+++ b/modules/local/run_alphafold2_msa.nf
@@ -44,7 +44,7 @@ process RUN_ALPHAFOLD2_MSA {
         alphafold2_model_preset += " --pdb70_database_path=${params.pdb70_dir_path}${params.pdb70_name} "
     }
     """
-    #if [ -f ${params.pdb_seqres_dir_path}/${params.pbd_seqres_txt_name} ]
+    #if [ -f ${params.pdb_seqres_dir_path}/${params.pdb_seqres_txt_name} ]
     #    \$PDB_SEQRES_TEMP=\$(mktemp --directory)
     #    cp ${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} \${PDB_SEQRES_TEMP}/
     #    then sed -i "/^\\w*0/d" \$PDB_SEQERS_TEMP/${params.pdb_seqres_txt_name}

From a0dbd9c7ac3aaa8dc78a0af61aa5ab755d7e82ff Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:37:28 +1000
Subject: [PATCH 15/22] feat(run_alphafold2): Added symlink for params file

---
 modules/local/run_alphafold2_pred.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf
index 9f6d20a7..cd7c93eb 100644
--- a/modules/local/run_alphafold2_pred.nf
+++ b/modules/local/run_alphafold2_pred.nf
@@ -38,7 +38,9 @@ process RUN_ALPHAFOLD2_PRED {
     def args = task.ext.args ?: ''
     """
     echo \$PWD
-    #if [ -d params/alphafold_params_* ]; then ln -r -s params/alphafold_params_*/* params/; fi
+    if [ -d ${params.alphafold2_db}/${params.alphafold2_params_path} ]; 
+        then ln -r -s params/alphafold_params_*/* params/
+    fi
     python3 /app/alphafold/run_predict.py \
         --fasta_paths=${fasta} \
         --model_preset=${alphafold2_model_preset} \

From 598cc269a40c52b7c1316aadffa7e6d34150a0eb Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:42:26 +1000
Subject: [PATCH 16/22] feat(nextflow): Changed default to use GPU

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 691ee289..8612912c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,7 +12,7 @@ params {
     // Input options
     input                       = null
     mode                        = 'alphafold2' // {alphafold2, colabfold}
-    use_gpu                     = false
+    use_gpu                     = true
 
     // Alphafold2 parameters
     alphafold2_mode             = "standard"

From eba441254ab202113940a48da7e5300d0ded1e69 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:44:15 +1000
Subject: [PATCH 17/22] feat(nextflow): Included katana config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 8612912c..775eb22a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -147,7 +147,7 @@ params {
 }
 
 // Load base.config by default for all pipelines
-includeConfig 'conf/base.config'
+includeConfig 'conf/katana.config'
 
 // Load nf-core custom profiles from different Institutions
 try {

From 4811d3cc235625b08a9930174332aef0840b44b1 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:44:54 +1000
Subject: [PATCH 18/22] feat(test): Added options to katana tests

---
 pf_files/proteinfold_test.sh | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pf_files/proteinfold_test.sh b/pf_files/proteinfold_test.sh
index 9e4883ce..3bdbc024 100755
--- a/pf_files/proteinfold_test.sh
+++ b/pf_files/proteinfold_test.sh
@@ -1,15 +1,16 @@
 module load nextflow/23.04.4 java/11
 
-export SINGULARITY_CACHE_DIR=/srv/scratch/sbf/singularity_cache
-export NXF_SINGULARITY_CACHEDIR=/srv/scratch/sbf/singularity_cache
+export SINGULARITY_CACHE_DIR=/srv/scratch/$USER/Singularity/cache
+export NXF_SINGULARITY_CACHEDIR=/srv/scratch/$USER/Singularity/cache
 
 nextflow run ../main.nf \
     --input samplesheet.csv \
     --outdir test_out \
     --mode alphafold2 \
-    --alphafold2_db /data/bio/alphafold \
+    --alphafold2_db /mnt/af2/ \
     --full_dbs true \
-    --alphafold2_model_preset monomer \
+    --alphafold2_model_preset multimer \
+    --alphafold_params_name 'params' \
     --alphafold2_mode 'split_msa_prediction' \
     --use_gpu true \
     -profile singularity \ 

From 92121114426ba67855a3c2245fa4d73647c4db59 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 14:48:56 +1000
Subject: [PATCH 19/22] revert(nextflow): Changed default GPU to false

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 775eb22a..c1a353e1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,7 +12,7 @@ params {
     // Input options
     input                       = null
     mode                        = 'alphafold2' // {alphafold2, colabfold}
-    use_gpu                     = true
+    use_gpu                     = false
 
     // Alphafold2 parameters
     alphafold2_mode             = "standard"

From 07954691cefc137e7f19ee271b3920c415b9ca84 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Fri, 16 Aug 2024 15:31:39 +1000
Subject: [PATCH 20/22] revert(nextflow): Changed config back to base config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index c1a353e1..691ee289 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -147,7 +147,7 @@ params {
 }
 
 // Load base.config by default for all pipelines
-includeConfig 'conf/katana.config'
+includeConfig 'conf/base.config'
 
 // Load nf-core custom profiles from different Institutions
 try {

From 5fe8e1df99ff1df65575a5d0ae757f3f19a2e19b Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 5 Sep 2024 16:02:24 +1000
Subject: [PATCH 21/22] feat(katana): Added katana config

---
 modules/local/run_alphafold2_pred.nf | 8 ++++----
 nextflow.config                      | 4 +++-
 pf_files/proteinfold_test.sh         | 2 +-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf
index cd7c93eb..9b371f86 100644
--- a/modules/local/run_alphafold2_pred.nf
+++ b/modules/local/run_alphafold2_pred.nf
@@ -9,7 +9,6 @@ process RUN_ALPHAFOLD2_PRED {
         'docker://nfcore/proteinfold_alphafold2_split:1.0.0' :
         'nfcore/proteinfold_alphafold2_split:1.0.0' }"
     echo 'true'
-
     input:
     tuple val(meta), path(fasta)
     val   db_preset
@@ -38,9 +37,10 @@ process RUN_ALPHAFOLD2_PRED {
     def args = task.ext.args ?: ''
     """
     echo \$PWD
-    if [ -d ${params.alphafold2_db}/${params.alphafold2_params_path} ]; 
-        then ln -r -s params/alphafold_params_*/* params/
-    fi
+    #if [ -d ${params.alphafold2_params_path} ]; 
+    #then
+    ln -r -f -s ${params.alphafold2_params_path}* params/
+    #fi
     python3 /app/alphafold/run_predict.py \
         --fasta_paths=${fasta} \
         --model_preset=${alphafold2_model_preset} \
diff --git a/nextflow.config b/nextflow.config
index 691ee289..69cc7ad2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -146,8 +146,10 @@ params {
 
 }
 
+spack.enabled = true
+
 // Load base.config by default for all pipelines
-includeConfig 'conf/base.config'
+includeConfig 'conf/katana.config'
 
 // Load nf-core custom profiles from different Institutions
 try {
diff --git a/pf_files/proteinfold_test.sh b/pf_files/proteinfold_test.sh
index 3bdbc024..396a63f1 100755
--- a/pf_files/proteinfold_test.sh
+++ b/pf_files/proteinfold_test.sh
@@ -1,4 +1,4 @@
-module load nextflow/23.04.4 java/11
+module load nextflow/23.04.4 java/11 cuda/11.8.0
 
 export SINGULARITY_CACHE_DIR=/srv/scratch/$USER/Singularity/cache
 export NXF_SINGULARITY_CACHEDIR=/srv/scratch/$USER/Singularity/cache

From 9af55b19269bca2fb9de8565ef1b71cac7d2a279 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 10 Oct 2024 12:24:32 +1100
Subject: [PATCH 22/22] feat(style): pushing uncommited changes

---
 modules/local/run_alphafold2.nf      | 40 +++++++++++++++++-----------
 modules/local/run_alphafold2_msa.nf  | 39 ++++++++++++++-------------
 modules/local/run_alphafold2_pred.nf | 23 ++++++++--------
 3 files changed, 57 insertions(+), 45 deletions(-)

diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf
index 30163279..013f3ed1 100644
--- a/modules/local/run_alphafold2.nf
+++ b/modules/local/run_alphafold2.nf
@@ -5,9 +5,12 @@ process RUN_ALPHAFOLD2 {
     tag "$meta.id"
     label 'process_medium'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://nfcore/proteinfold_alphafold2_standard:1.0.0' :
-        'nfcore/proteinfold_alphafold2_standard:1.0.0' }"
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local RUN_ALPHAFOLD2 module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
+    container "nf-core/proteinfold_alphafold2_standard:1.1.1"
 
     input:
     tuple val(meta), path(fasta)
@@ -19,7 +22,7 @@ process RUN_ALPHAFOLD2 {
     path ('mgnify/*')
     path ('pdb70/*')
     path ('pdb_mmcif/*')
-    path ('uniclust30/*')
+    path ('uniref30/*')
     path ('uniref90/*')
     path ('pdb_seqres/*')
     path ('uniprot/*')
@@ -34,31 +37,35 @@ process RUN_ALPHAFOLD2 {
 
     script:
     def args = task.ext.args ?: ''
-    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_dir_path}${params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name} --uniclust30_database_path=${params.uniclust30_dir_path}${params.uniclust30_db_name}" :
-        "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}${params.bfd_first_non_consensus_sequences_name}"
+    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.alphafold2_db}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniref30_database_path=${params.alphafold2_db}/uniref30/UniRef30_2021_03" :
+        "reduced_dbs --small_bfd_database_path=${params.alphafold2_db}/small_bfd/bfd-first_non_consensus_sequences.fasta"
     if (alphafold2_model_preset == 'multimer') {
-        alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} --uniprot_database_path=${params.uniprot_dir_path}${params.uniprot_fasta_name} "
+        alphafold2_model_preset += " --pdb_seqres_database_path=${params.alphafold2_db}/pdb_seqres/pdb_seqres.txt --uniprot_database_path=${params.alphafold2_db}/uniprot/uniprot.fasta "
     }
     else {
-        alphafold2_model_preset += " --pdb70_database_path=${params.pdb_dir_path}${params.pdb70_name} "
+        alphafold2_model_preset += " --pdb70_database_path=${params.alphafold2_db}/pdb70/pdb70_from_mmcif_200916/pdb70 "
     }
     """
-    if [ -f ${params.pdb_seqres_dir_path}/${params.pdb_seqres_txt_name} ]
-        \$PDB_SEQRES_TEMP=\$(mktemp --directory)
-        cp ${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} \${PDB_SEQRES_TEMP}/
-        then sed -i "/^\\w*0/d" \$PDB_SEQERS_TEMP/${params.pdb_seqres_txt_name}
+    RUNTIME_TMP=\$(mktemp -d)
+    nvcc --version 2>&1 | tee /home/z3545907/nvcc.txt
+    nvidia-smi 2>&1 | tee /home/z3545907/nvidia-smi.txt
+    if [ -f ${params.alphafold2_db}/pdb_seqres/pdb_seqres.txt ]
+        cp ${params.alphafold2_db}/pdb_seqres/pdb_seqres.txt \${RUNTIME_TMP}
+        then sed -i "/^\\w*0/d" \${RUNTIME_TMP}/pdb_seqres.txt
     fi
-    if [ -d ${params.alphafold2_params_path} ]; then ln -r -s ${params.alphafold2_params_path} params/; fi
+    if [ -d ${params.alphafold2_db}/params/ ]; then ln -r -s ${params.alphafold2_db}/params params; fi
     python3 /app/alphafold/run_alphafold.py \
         --fasta_paths=${fasta} \
         --model_preset=${alphafold2_model_preset} \
         --db_preset=${db_preset} \
         --output_dir=\$PWD \
         --data_dir=\$PWD \
-        --uniref90_database_path=${params.uniref90_dir_path}uniref90.fasta \
-        --template_mmcif_dir=${params.template_mmcif_dir} \
-        --obsolete_pdbs_path=${params.obsolete_pdbs_path} \
+        --uniref90_database_path=${params.alphafold2_db}/uniref90/uniref90.fasta \
+        --mgnify_database_path=${params.alphafold2_db}/mgnify/mgy_clusters_2022_05.fa \
+        --template_mmcif_dir=${params.alphafold2_db}/pdb_mmcif/mmcif_files \
+        --obsolete_pdbs_path=${params.alphafold2_db}/pdb_mmcif/obsolete.dat \
         --random_seed=53343 \
+        --use_gpu_relax \
         $args
 
     cp "${fasta.baseName}"/ranked_0.pdb ./"${fasta.baseName}".alphafold.pdb
@@ -71,6 +78,7 @@ process RUN_ALPHAFOLD2 {
     echo -e Positions"\\t"rank_0"\\t"rank_1"\\t"rank_2"\\t"rank_3"\\t"rank_4 > header.tsv
     cat header.tsv plddt.tsv > ../"${fasta.baseName}"_plddt_mqc.tsv
     cd ..
+    rm -rf "\${RUNTIME_TMP}"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf
index d4fa4f53..7878d9d1 100644
--- a/modules/local/run_alphafold2_msa.nf
+++ b/modules/local/run_alphafold2_msa.nf
@@ -4,11 +4,13 @@
 process RUN_ALPHAFOLD2_MSA {
     tag   "$meta.id"
     label 'process_medium'
-    debug true
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://nfcore/proteinfold_alphafold2_msa:1.0.0' :
-        'nfcore/proteinfold_alphafold2_msa:1.0.0' }"
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local RUN_ALPHAFOLD2_MSA module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
+    container "nf-core/proteinfold_alphafold2_msa:1.1.1"
 
     input:
     tuple val(meta), path(fasta)
@@ -20,7 +22,7 @@ process RUN_ALPHAFOLD2_MSA {
     path ('mgnify/*')
     path ('pdb70/*')
     path ('pdb_mmcif/*')
-    path ('uniclust30/*')
+    path ('uniref30/*')
     path ('uniref90/*')
     path ('pdb_seqres/*')
     path ('uniprot/*')
@@ -35,33 +37,34 @@ process RUN_ALPHAFOLD2_MSA {
 
     script:
     def args = task.ext.args ?: ''
-    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.bfd_dir_path}${params.bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name} --uniclust30_database_path=${params.uniclust30_dir_path}${params.uniclust30_db_name}" :
-        "reduced_dbs --small_bfd_database_path=${params.small_bfd_path}${params.bfd_first_non_consensus_sequences_name}"
+    def db_preset = db_preset ? "full_dbs --bfd_database_path=${params.alphafold2_db}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniref30_database_path=${params.alphafold2_db}/uniref30/UniRef30_2021_03" :
+        "reduced_dbs --small_bfd_database_path=${params.alphafold2_db}/small_bfd/bfd-first_non_consensus_sequences.fasta"
     if (alphafold2_model_preset == 'multimer') {
-        alphafold2_model_preset += " --pdb_seqres_database_path=${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} --uniprot_database_path=${params.uniprot_dir_path}/${params.uniprot_fasta_name} "
+        alphafold2_model_preset += " --pdb_seqres_database_path=${params.alphafold2_db}/pdb_seqres/pdb_seqres.txt --uniprot_database_path=${params.alphafold2_db}/uniprot/uniprot.fasta "
     }
     else {
-        alphafold2_model_preset += " --pdb70_database_path=${params.pdb70_dir_path}${params.pdb70_name} "
+        alphafold2_model_preset += " --pdb70_database_path=${params.alphafold2_db}/pdb70/pdb70_from_mmcif_200916/pdb70 "
     }
     """
-    #if [ -f ${params.pdb_seqres_dir_path}/${params.pdb_seqres_txt_name} ]
-    #    \$PDB_SEQRES_TEMP=\$(mktemp --directory)
-    #    cp ${params.pdb_seqres_dir_path}${params.pdb_seqres_txt_name} \${PDB_SEQRES_TEMP}/
-    #    then sed -i "/^\\w*0/d" \$PDB_SEQERS_TEMP/${params.pdb_seqres_txt_name}
-    #fi
+    RUNTIME_TMP=\$(mktemp -d)
+    if [ -f ${params.alphafold2_db}/pdb_seqres/pdb_seqres.txt ]
+        cp ${params.alphafold2_db}/pdb_seqres/pdb_seqres.txt \${RUNTIME_TMP}
+        then sed -i "/^\\w*0/d" \${RUNTIME_TMP}/pdb_seqres.txt
+    fi
     python3 /app/alphafold/run_msa.py \
         --fasta_paths=${fasta} \
         --model_preset=${alphafold2_model_preset} \
         --db_preset=${db_preset} \
         --output_dir=\$PWD \
         --data_dir=\$PWD \
-        --uniref90_database_path=${params.uniref90_dir_path}/${params.uniref90_fasta_name} \
-        --mgnify_database_path=${params.mgnify_database_path}/${params.mgy_clusters_fasta_name} \
-        --template_mmcif_dir=${params.template_mmcif_dir} \
-        --obsolete_pdbs_path=${params.obsolete_pdbs_path}  \
+        --uniref90_database_path=${params.alphafold2_db}/uniref90/uniref90.fasta \
+        --mgnify_database_path=${params.alphafold2_db}/mgnify/mgy_clusters_2022_05.fa \
+        --template_mmcif_dir=${params.alphafold2_db}/pdb_mmcif/mmcif_files \
+        --obsolete_pdbs_path=${params.alphafold2_db}/pdb_mmcif/obsolete.dat  \
         $args
 
     cp "${fasta.baseName}"/features.pkl ./"${fasta.baseName}".features.pkl
+    rm -rf "\${RUNTIME_TMP}"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf
index 9b371f86..3f34c95f 100644
--- a/modules/local/run_alphafold2_pred.nf
+++ b/modules/local/run_alphafold2_pred.nf
@@ -3,12 +3,16 @@
  */
 process RUN_ALPHAFOLD2_PRED {
     tag   "$meta.id"
-    label 'process_medium', 'gpu_compute'
+    label 'process_medium'
+    label 'gpu_compute'
+
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local RUN_ALPHAFOLD2_PRED module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
+
+    container "nf-core/proteinfold_alphafold2_split:1.1.1"
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://nfcore/proteinfold_alphafold2_split:1.0.0' :
-        'nfcore/proteinfold_alphafold2_split:1.0.0' }"
-    echo 'true'
     input:
     tuple val(meta), path(fasta)
     val   db_preset
@@ -19,7 +23,7 @@ process RUN_ALPHAFOLD2_PRED {
     path ('mgnify/*')
     path ('pdb70/*')
     path ('pdb_mmcif/*')
-    path ('uniclust30/*')
+    path ('uniref30/*')
     path ('uniref90/*')
     path ('pdb_seqres/*')
     path ('uniprot/*')
@@ -36,11 +40,7 @@ process RUN_ALPHAFOLD2_PRED {
     script:
     def args = task.ext.args ?: ''
     """
-    echo \$PWD
-    #if [ -d ${params.alphafold2_params_path} ]; 
-    #then
-    ln -r -f -s ${params.alphafold2_params_path}* params/
-    #fi
+    if [ -d ${params.alphafold2_db}/params/ ]; then ln -r -s ${params.alphafold2_db}/params params; fi
     python3 /app/alphafold/run_predict.py \
         --fasta_paths=${fasta} \
         --model_preset=${alphafold2_model_preset} \
@@ -48,6 +48,7 @@ process RUN_ALPHAFOLD2_PRED {
         --data_dir=\$PWD \
         --random_seed=53343 \
         --msa_path=${msa} \
+        --use_gpu_relax \
         $args
 
     cp "${fasta.baseName}"/ranked_0.pdb ./"${fasta.baseName}".alphafold.pdb