ci - auto build from bactopia

Author: rpetit3

docs/bactopia-tools/abricate.md

@@ -158,8 +158,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/abritamr.md

@@ -169,8 +169,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/agrvate.md

@@ -167,8 +167,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/amrfinderplus.md

@@ -148,6 +148,7 @@ Use these parameters to specify which samples to include or exclude.
 | <i class="fa-lg fas fa-expand-arrows-alt"></i>` --report_common` | Report proteins common to a taxonomy group <br/>**Type:** `boolean` |
 | <i class="fa-lg fas fa-expand-arrows-alt"></i>` --report_all_equal` | Report all equally-scoring BLAST and HMM matches <br/>**Type:** `boolean` |
 | <i class="fa-lg fas fa-expand-arrows-alt"></i>` --amrfinder_opts` | Extra AMRFinder+ options in quotes. <br/>**Type:** `string` |
+| <i class="fa-lg fas fa-expand-arrows-alt"></i>` --amrfinder_db` | A custom AMRFinder+ database to use, either a tarball or a folder <br/>**Type:** `string` |
 
 
 ### <i class="fa-xl fa-solid fa-gears"></i> Optional Parameters
@@ -167,8 +168,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/ariba.md

@@ -193,8 +193,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/bakta.md

@@ -188,8 +188,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/blastn.md

@@ -163,8 +163,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/blastp.md

@@ -161,8 +161,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/blastx.md

@@ -161,8 +161,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters

docs/bactopia-tools/bracken.md

@@ -175,8 +175,8 @@ Set the top limit for requested resources for any single job.
 |:---|---|
 | <i class="fa-lg fas fa-redo"></i>` --max_retry` | Maximum times to retry a process before allowing it to fail. <br/>**Type:** `integer`, **Default:** `3` |
 | <i class="fa-lg fas fa-microchip"></i>` --max_cpus` | Maximum number of CPUs that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `4` |
-| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory (in GB) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `32` |
-| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time (in minutes) that can be requested for any single job. <br/>**Type:** `integer`, **Default:** `120` |
+| <i class="fa-lg fas fa-memory"></i>` --max_memory` | Maximum amount of memory that can be requested for any single job. <br/>**Type:** `string`, **Default:** `128.GB` |
+| <i class="fa-lg far fa-clock"></i>` --max_time` | Maximum amount of time that can be requested for any single job. <br/>**Type:** `string`, **Default:** `240.h` |
 | <i class="fa-lg fas fa-angle-double-up"></i>` --max_downloads` | Maximum number of samples to download at a time <br/>**Type:** `integer`, **Default:** `3` |
 
 ### <i class="fa-xl fa-solid fa-screwdriver-wrench"></i> Nextflow Configuration Parameters