diff --git a/docs/usage.md b/docs/usage.md
index cd9a5c588..56aa6d688 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -26,16 +26,16 @@ Each task is controlled by one of the following commands: `run`, `rerun`, `runp`
 Here you can see the command-line usage instructions for the main looper command and for each subcommand:
 ## `looper --help`
 ```console
-version: 1.2.0-dev
-usage: looper [-h] [--version] [--logfile LOGFILE] [--verbosity {0,1,2,3,4}]
-              [--dbg]
-              {run,rerun,runp,table,report,destroy,check,clean,inspect,init}
+version: 1.4.0-dev
+usage: looper [-h] [--version] [--logfile LOGFILE] [--dbg] [--silent]
+              [--verbosity V] [--logdev]
+              {run,rerun,runp,table,report,destroy,check,clean,inspect,init,init-piface}
               ...
 
 looper - A project job submission engine and project manager.
 
 positional arguments:
-  {run,rerun,runp,table,report,destroy,check,clean,inspect,init}
+  {run,rerun,runp,table,report,destroy,check,clean,inspect,init,init-piface}
     run                 Run or submit sample jobs.
     rerun               Resubmit sample jobs with failed flags.
     runp                Run or submit project jobs.
@@ -46,14 +46,16 @@ positional arguments:
     clean               Run clean scripts of already processed jobs.
     inspect             Print information about a project.
     init                Initialize looper dotfile.
+    init-piface         Initialize generic pipeline interface.
 
-optional arguments:
+options:
   -h, --help            show this help message and exit
   --version             show program's version number and exit
   --logfile LOGFILE     Optional output file for looper logs (default: None)
-  --verbosity {0,1,2,3,4}
-                        Choose level of verbosity (default: None)
   --dbg                 Turn on debug mode (default: False)
+  --silent              Silence logging. Overrides verbosity.
+  --verbosity V         Set logging level (1-5 or logging module level name)
+  --logdev              Expand content of logging message format.
 
 For subcommand-specific options, type: 'looper <subcommand> -h'
 https://github.com/pepkit/looper
@@ -61,35 +63,39 @@ https://github.com/pepkit/looper
 
 ## `looper run --help`
 ```console
-usage: looper run [-h] [-i] [-d] [-t S] [-l N] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P]
-                  [-s S] [-c K [K ...]] [-u X] [-n N] [-g K] [--sel-attr ATTR]
-                  [--sel-excl [E [E ...]] | --sel-incl [I [I ...]]] [-a A [A ...]]
+usage: looper run [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P] [-s S]
+                  [-c K [K ...]] [-u X] [-n N] [-S YAML [YAML ...]] [-P YAML [YAML ...]]
+                  [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl
+                  [I ...]] [-a A [A ...]]
                   [config_file]
 
 Run or submit sample jobs.
 
 positional arguments:
-  config_file                        Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
+options:
   -h, --help                         show this help message and exit
   -i, --ignore-flags                 Ignore run status flags? Default=False
   -d, --dry-run                      Don't actually submit the jobs. Default=False
   -t S, --time-delay S               Time delay in seconds between job submissions
-  -l N, --limit N                    Limit to n samples
   -x S, --command-extra S            String to append to every command
   -y S, --command-extra-override S   Same as command-extra, but overrides values in PEP
   -f, --skip-file-checks             Do not perform input file checks
   -u X, --lump X                     Total input file size (GB) to batch into one job
   -n N, --lumpn N                    Number of commands to batch into one job
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
   -a A [A ...], --amend A [A ...]    List of amendments to activate
 
 divvy arguments:
   Configure divvy to change computing settings
 
   --divvy DIVCFG                     Path to divvy configuration file. Default=$DIVCFG env
-                                     variable. Currently: /Users/mstolarczyk/Uczelnia/UVA/
-                                     code//divcfg/uva_rivanna.yaml
+                                     variable. Currently: not set
   -p P, --package P                  Name of computing resource package to use
   -s S, --settings S                 Path to a YAML settings file with compute settings
   -c K [K ...], --compute K [K ...]  List of key-value pairs (k1=v1)
@@ -97,41 +103,46 @@ divvy arguments:
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K               Sample attribute specifying toggle. Default: toggle
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
   --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]             Exclude samples with these values
-  --sel-incl [I [I ...]]             Include only samples with these values
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
 
 ## `looper runp --help`
 ```console
-usage: looper runp [-h] [-i] [-d] [-t S] [-l N] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P]
-                   [-s S] [-c K [K ...]] [-g K] [--sel-attr ATTR] [--sel-excl [E [E ...]]
-                   | --sel-incl [I [I ...]]] [-a A [A ...]]
+usage: looper runp [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P] [-s S]
+                   [-c K [K ...]] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N]
+                   [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]]
+                   [-a A [A ...]]
                    [config_file]
 
 Run or submit project jobs.
 
 positional arguments:
-  config_file                        Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
+options:
   -h, --help                         show this help message and exit
   -i, --ignore-flags                 Ignore run status flags? Default=False
   -d, --dry-run                      Don't actually submit the jobs. Default=False
   -t S, --time-delay S               Time delay in seconds between job submissions
-  -l N, --limit N                    Limit to n samples
   -x S, --command-extra S            String to append to every command
   -y S, --command-extra-override S   Same as command-extra, but overrides values in PEP
   -f, --skip-file-checks             Do not perform input file checks
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
   -a A [A ...], --amend A [A ...]    List of amendments to activate
 
 divvy arguments:
   Configure divvy to change computing settings
 
   --divvy DIVCFG                     Path to divvy configuration file. Default=$DIVCFG env
-                                     variable. Currently: /Users/mstolarczyk/Uczelnia/UVA/
-                                     code//divcfg/uva_rivanna.yaml
+                                     variable. Currently: not set
   -p P, --package P                  Name of computing resource package to use
   -s S, --settings S                 Path to a YAML settings file with compute settings
   -c K [K ...], --compute K [K ...]  List of key-value pairs (k1=v1)
@@ -139,43 +150,48 @@ divvy arguments:
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K               Sample attribute specifying toggle. Default: toggle
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
   --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]             Exclude samples with these values
-  --sel-incl [I [I ...]]             Include only samples with these values
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
 
 ## `looper rerun --help`
 ```console
-usage: looper rerun [-h] [-i] [-d] [-t S] [-l N] [-x S] [-y S] [-f] [--divvy DIVCFG]
-                    [-p P] [-s S] [-c K [K ...]] [-u X] [-n N] [-g K] [--sel-attr ATTR]
-                    [--sel-excl [E [E ...]] | --sel-incl [I [I ...]]] [-a A [A ...]]
+usage: looper rerun [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P]
+                    [-s S] [-c K [K ...]] [-u X] [-n N] [-S YAML [YAML ...]]
+                    [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR]
+                    [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]]
                     [config_file]
 
 Resubmit sample jobs with failed flags.
 
 positional arguments:
-  config_file                        Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
+options:
   -h, --help                         show this help message and exit
   -i, --ignore-flags                 Ignore run status flags? Default=False
   -d, --dry-run                      Don't actually submit the jobs. Default=False
   -t S, --time-delay S               Time delay in seconds between job submissions
-  -l N, --limit N                    Limit to n samples
   -x S, --command-extra S            String to append to every command
   -y S, --command-extra-override S   Same as command-extra, but overrides values in PEP
   -f, --skip-file-checks             Do not perform input file checks
   -u X, --lump X                     Total input file size (GB) to batch into one job
   -n N, --lumpn N                    Number of commands to batch into one job
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
   -a A [A ...], --amend A [A ...]    List of amendments to activate
 
 divvy arguments:
   Configure divvy to change computing settings
 
   --divvy DIVCFG                     Path to divvy configuration file. Default=$DIVCFG env
-                                     variable. Currently: /Users/mstolarczyk/Uczelnia/UVA/
-                                     code//divcfg/uva_rivanna.yaml
+                                     variable. Currently: not set
   -p P, --package P                  Name of computing resource package to use
   -s S, --settings S                 Path to a YAML settings file with compute settings
   -c K [K ...], --compute K [K ...]  List of key-value pairs (k1=v1)
@@ -183,178 +199,232 @@ divvy arguments:
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K               Sample attribute specifying toggle. Default: toggle
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
   --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]             Exclude samples with these values
-  --sel-incl [I [I ...]]             Include only samples with these values
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
 
 ## `looper report --help`
 ```console
-usage: looper report [-h] [-g K] [--sel-attr ATTR] [--sel-excl [E [E ...]] | --sel-incl
-                     [I [I ...]]] [-a A [A ...]]
+usage: looper report [-h] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N]
+                     [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]]
+                     [-a A [A ...]] [--project]
                      [config_file]
 
 Create browsable HTML report of project results.
 
 positional arguments:
-  config_file                      Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
-  -h, --help                       show this help message and exit
-  -a A [A ...], --amend A [A ...]  List of amendments to activate
+options:
+  -h, --help                         show this help message and exit
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
+  -a A [A ...], --amend A [A ...]    List of amendments to activate
+  --project                          Process project-level pipelines
 
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K             Sample attribute specifying toggle. Default: toggle
-  --sel-attr ATTR                  Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]           Exclude samples with these values
-  --sel-incl [I [I ...]]           Include only samples with these values
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
+  --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
 
 ## `looper table --help`
 ```console
-usage: looper table [-h] [-g K] [--sel-attr ATTR] [--sel-excl [E [E ...]] | --sel-incl
-                    [I [I ...]]] [-a A [A ...]]
+usage: looper table [-h] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N]
+                    [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]]
+                    [-a A [A ...]] [--project]
                     [config_file]
 
 Write summary stats table for project samples.
 
 positional arguments:
-  config_file                      Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
-  -h, --help                       show this help message and exit
-  -a A [A ...], --amend A [A ...]  List of amendments to activate
+options:
+  -h, --help                         show this help message and exit
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
+  -a A [A ...], --amend A [A ...]    List of amendments to activate
+  --project                          Process project-level pipelines
 
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K             Sample attribute specifying toggle. Default: toggle
-  --sel-attr ATTR                  Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]           Exclude samples with these values
-  --sel-incl [I [I ...]]           Include only samples with these values
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
+  --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
 
 ## `looper inspect --help`
 ```console
-usage: looper inspect [-h] [-n S [S ...]] [-l L] [-g K] [--sel-attr ATTR]
-                      [--sel-excl [E [E ...]] | --sel-incl [I [I ...]]] [-a A [A ...]]
+usage: looper inspect [-h] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N]
+                      [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]]
+                      [-a A [A ...]] [--sample-names [SAMPLE_NAMES ...]]
+                      [--attr-limit ATTR_LIMIT]
                       [config_file]
 
 Print information about a project.
 
 positional arguments:
-  config_file                       Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
-  -h, --help                        show this help message and exit
-  -n S [S ...], --snames S [S ...]  Name of the samples to inspect
-  -l L, --attr-limit L              Number of sample attributes to display
-  -a A [A ...], --amend A [A ...]   List of amendments to activate
+options:
+  -h, --help                         show this help message and exit
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
+  -a A [A ...], --amend A [A ...]    List of amendments to activate
+  --sample-names [SAMPLE_NAMES ...]  Names of the samples to inspect
+  --attr-limit ATTR_LIMIT            Number of attributes to display
 
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K              Sample attribute specifying toggle. Default: toggle
-  --sel-attr ATTR                   Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]            Exclude samples with these values
-  --sel-incl [I [I ...]]            Include only samples with these values
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
+  --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
 
 ## `looper init --help`
 ```console
-usage: looper init [-h] [-f] config_file
+usage: looper init [-h] [-f] [-o DIR] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-p]
+                   config_file
 
 Initialize looper dotfile.
 
 positional arguments:
-  config_file  Project configuration file (YAML)
+  config_file                        Project configuration file (YAML)
 
-optional arguments:
-  -h, --help   show this help message and exit
-  -f, --force  Force overwrite
+options:
+  -h, --help                         show this help message and exit
+  -f, --force                        Force overwrite
+  -o DIR, --output-dir DIR
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
+  -p, --piface                       Generates generic pipeline interface
 ```
 
 ## `looper destroy --help`
 ```console
-usage: looper destroy [-h] [-d] [--force-yes] [-g K] [--sel-attr ATTR]
-                      [--sel-excl [E [E ...]] | --sel-incl [I [I ...]]] [-a A [A ...]]
+usage: looper destroy [-h] [-d] [--force-yes] [-S YAML [YAML ...]] [-P YAML [YAML ...]]
+                      [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl
+                      [I ...]] [-a A [A ...]]
                       [config_file]
 
 Remove output files of the project.
 
 positional arguments:
-  config_file                      Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
-  -h, --help                       show this help message and exit
-  -d, --dry-run                    Don't actually submit the jobs. Default=False
-  --force-yes                      Provide upfront confirmation of destruction intent, to
-                                   skip console query. Default=False
-  -a A [A ...], --amend A [A ...]  List of amendments to activate
+options:
+  -h, --help                         show this help message and exit
+  -d, --dry-run                      Don't actually submit the jobs. Default=False
+  --force-yes                        Provide upfront confirmation of destruction intent,
+                                     to skip console query. Default=False
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
+  -a A [A ...], --amend A [A ...]    List of amendments to activate
 
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K             Sample attribute specifying toggle. Default: toggle
-  --sel-attr ATTR                  Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]           Exclude samples with these values
-  --sel-incl [I [I ...]]           Include only samples with these values
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
+  --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
 
 ## `looper check --help`
 ```console
-usage: looper check [-h] [-A] [-f [F [F ...]]] [-g K] [--sel-attr ATTR]
-                    [--sel-excl [E [E ...]] | --sel-incl [I [I ...]]] [-a A [A ...]]
+usage: looper check [-h] [--describe-codes] [--itemized] [-f [F ...]] [-S YAML [YAML ...]]
+                    [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR]
+                    [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] [--project]
                     [config_file]
 
 Check flag status of current runs.
 
 positional arguments:
-  config_file                        Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
+options:
   -h, --help                         show this help message and exit
-  -A, --all-folders                  Check status for all output folders, not just for
-                                     samples specified in the config. Default=False
-  -f [F [F ...]], --flags [F [F ...]]
-                                     Check on only these flags/status values
+  --describe-codes                   Show status codes description
+  --itemized                         Show a detailed, by sample statuses
+  -f [F ...], --flags [F ...]        Check on only these flags/status values
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
   -a A [A ...], --amend A [A ...]    List of amendments to activate
+  --project                          Process project-level pipelines
 
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K               Sample attribute specifying toggle. Default: toggle
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
   --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]             Exclude samples with these values
-  --sel-incl [I [I ...]]             Include only samples with these values
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
 
 ## `looper clean --help`
 ```console
-usage: looper clean [-h] [-d] [--force-yes] [-g K] [--sel-attr ATTR]
-                    [--sel-excl [E [E ...]] | --sel-incl [I [I ...]]] [-a A [A ...]]
+usage: looper clean [-h] [-d] [--force-yes] [-S YAML [YAML ...]] [-P YAML [YAML ...]]
+                    [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl
+                    [I ...]] [-a A [A ...]]
                     [config_file]
 
 Run clean scripts of already processed jobs.
 
 positional arguments:
-  config_file                      Project configuration file (YAML)
+  config_file                        Project configuration file (YAML) or pephub registry
+                                     path.
 
-optional arguments:
-  -h, --help                       show this help message and exit
-  -d, --dry-run                    Don't actually submit the jobs. Default=False
-  --force-yes                      Provide upfront confirmation of destruction intent, to
-                                   skip console query. Default=False
-  -a A [A ...], --amend A [A ...]  List of amendments to activate
+options:
+  -h, --help                         show this help message and exit
+  -d, --dry-run                      Don't actually submit the jobs. Default=False
+  --force-yes                        Provide upfront confirmation of destruction intent,
+                                     to skip console query. Default=False
+  -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper sample config file
+  -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...]
+                                     Path to looper project config file
+  -a A [A ...], --amend A [A ...]    List of amendments to activate
 
 sample selection arguments:
   Specify samples to include or exclude based on sample attribute values
 
-  -g K, --toggle-key K             Sample attribute specifying toggle. Default: toggle
-  --sel-attr ATTR                  Attribute for sample exclusion OR inclusion
-  --sel-excl [E [E ...]]           Exclude samples with these values
-  --sel-incl [I [I ...]]           Include only samples with these values
+  -l N, --limit N                    Limit to n samples
+  -k N, --skip N                     Skip samples by numerical index
+  --sel-attr ATTR                    Attribute for sample exclusion OR inclusion
+  --sel-excl [E ...]                 Exclude samples with these values
+  --sel-incl [I ...]                 Include only samples with these values
 ```
+
diff --git a/looper/looper.py b/looper/looper.py
index ebbb82bda..fa3c62696 100755
--- a/looper/looper.py
+++ b/looper/looper.py
@@ -577,28 +577,20 @@ def __call__(self, args):
         # initialize the report builder
         p = self.prj
         project_level = args.project
+
         if project_level:
-            html_report_builder_project = HTMLReportBuilderProject(prj=p)
-            self.counter = LooperCounter(len(p.project_pipeline_interfaces))
-            for piface in p.project_pipeline_interface_sources:
-                pn = PipelineInterface(piface).pipeline_name
-                _LOGGER.info(
-                    self.counter.show(name=p.name, type="project", pipeline_name=pn)
-                )
-                # Do the stats and object summarization.
-                # run the report builder. a set of HTML pages is produced
-                report_path = html_report_builder_project(piface_source=piface)
-                _LOGGER.info(
-                    f"Project-level pipeline '{pn}' HTML report: {report_path}"
-                )
+            psms = self.prj.get_pipestat_managers(project_level=True)
+            print(psms)
+            for name, psm in psms.items():
+                # Summarize will generate the static HTML Report Function
+                psm.summarize()
         else:
-            html_report_builder = HTMLReportBuilder(prj=self.prj)
-            for sample_piface_source in self.prj.pipeline_interface_sources:
-                # Do the stats and object summarization.
-                pn = PipelineInterface(sample_piface_source).pipeline_name
-                # run the report builder. a set of HTML pages is produced
-                report_path = html_report_builder(pipeline_name=pn)
-                _LOGGER.info(f"Sample-level pipeline '{pn}' HTML report: {report_path}")
+            for sample in p.prj.samples:
+                psms = self.prj.get_pipestat_managers(sample_name=sample.sample_name)
+                print(psms)
+                for name, psm in psms.items():
+                    # Summarize will generate the static HTML Report Function
+                    psm.summarize()
 
 
 class Tabulator(Executor):
diff --git a/looper/project.py b/looper/project.py
index 1085f1b94..84d2006a2 100644
--- a/looper/project.py
+++ b/looper/project.py
@@ -490,7 +490,7 @@ def _get_val_from_attr(pipestat_sect, object, attr_name, default, no_err=False):
             :return str: retrieved configuration value
             """
             if pipestat_sect is not None and attr_name in pipestat_sect:
-                return getattr(object, pipestat_sect[attr_name])
+                return pipestat_sect[attr_name]
             try:
                 return getattr(object, default)
             except AttributeError:
@@ -527,13 +527,7 @@ def _get_val_from_attr(pipestat_sect, object, attr_name, default, no_err=False):
         )
 
         pipestat_config = self._resolve_path_with_cfg(pth=pipestat_config)
-        namespace = _get_val_from_attr(
-            pipestat_section,
-            self.config if project_level else self.get_sample(sample_name),
-            PIPESTAT_NAMESPACE_ATTR_KEY,
-            "name" if project_level else self.sample_table_index,
-            pipestat_config and os.path.exists(pipestat_config),
-        )
+
         results_file_path = _get_val_from_attr(
             pipestat_section,
             self.config if project_level else self.get_sample(sample_name),
@@ -557,10 +551,9 @@ def _get_val_from_attr(pipestat_sect, object, attr_name, default, no_err=False):
                 else f"{piface.pipeline_name}_{'_'.join(self.amendments)}"
             )
             ret[piface.pipeline_name] = {
-                "namespace": namespace,
-                "config": pipestat_config,
+                "config_file": pipestat_config,
                 "results_file_path": results_file_path,
-                "record_identifier": rec_id,
+                "sample_name": rec_id,
                 "schema_path": piface.get_pipeline_schemas(OUTPUT_SCHEMA_KEY),
             }
         return ret
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 19afd0728..64d948682 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -6,7 +6,7 @@ logmuse>=0.2.0
 pandas>=2.0.2
 pephubclient
 peppy>=0.35.4
-pipestat>=0.1.0
+pipestat>=0.4.0
 pyyaml>=3.12
 rich>=9.10.0
 ubiquerg>=0.5.2